Resource List
List all resources, or create a new resource.
GET /api/t/?format=api&output=%22Sequence+alignment%22
{ "count": 232, "next": "?page=2", "previous": null, "list": [ { "name": "nallo", "description": "Nallo is a bioinformatics analysis pipeline for long-reads from both PacBio and (targeted) ONT-data, focused on rare-disease. The pipeline detects a wide range of genetic variants, performs genome assembly,\nand reports CpG methylation. It also enables annotation and ranking of variants based on their predicted functional\nconsequences.", "homepage": "https://github.com/genomic-medicine-sweden/nallo", "biotoolsID": "nallo", "biotoolsCURIE": "biotools:nallo", "version": [ "0.12.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3227", "term": "Variant calling" }, { "uri": "http://edamontology.org/operation_0331", "term": "Variant effect prediction" }, { "uri": "http://edamontology.org/operation_0525", "term": "Genome assembly" }, { "uri": "http://edamontology.org/operation_3226", "term": "Variant prioritisation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" }, { "uri": "http://edamontology.org/format_3752", "term": "CSV" }, { "uri": "http://edamontology.org/format_2572", "term": "BAM" }, { "uri": "http://edamontology.org/format_2545", "term": "FASTQ-like format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_3462", "term": "CRAM" }, { "uri": "http://edamontology.org/format_2572", "term": "BAM" }, { "uri": "http://edamontology.org/format_3327", "term": "BAI" } ] } ], "note": null, "cmd": null } ], "toolType": [], "topic": [ { "uri": "http://edamontology.org/topic_0769", "term": "Workflows" }, { "uri": "http://edamontology.org/topic_0196", "term": "Sequence assembly" }, { "uri": "http://edamontology.org/topic_3673", "term": "Whole genome sequencing" }, { "uri": "http://edamontology.org/topic_0749", "term": "Transcription factors and regulatory sites" }, { "uri": "http://edamontology.org/topic_3295", "term": "Epigenetics" } ], "operatingSystem": [], "language": [ "Groovy", "Java" ], "license": "MIT", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/genomic-medicine-sweden/nallo", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [ { "url": "https://genomic-medicine-sweden.github.io/nallo/latest/", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1093/BIOINFORMATICS/BTAG086", "pmid": "41712762", "pmcid": "PMC12988770", "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Lars Feuk", "email": "lars.feuk@igp.uu.se", "url": null, "orcidid": "https://orcid.org/0000-0003-2355-2919", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "owner": "juan_camilo", "additionDate": "2026-06-12T12:09:48.272845Z", "lastUpdate": "2026-06-12T14:03:07.797466Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "ProteinsPlus", "description": "The ProteinsPlus web server aims to support life scientists in working with protein structures. Protein structures are the key to understanding protein function. They are an important resource in many biotechnological application areas from pharmaceutical research to biocatalysis. ProteinsPlus focuses on protein-ligand interactions. The server provides support for the initial steps of dealing with protein structures, namely structure search, quality assessment, and preprocessing. JAMDA enables users to perform an on-the-fly molecular docking of up to five molecules. The poses can then be visualized in 2D (PoseView, PoseEdit). Furthermore, advanced options, such as protein pocket detection (DoGSite), prediction of water molecule positions (WarPP), protein structure ensemble generation (SIENA), prediction of metal coordination (METALizer), the analysis of solvent channels in protein crystals (LifeSoaks), or the categorization of protein-protein-interfaces (HyPPI) are supported.", "homepage": "https://proteins.plus", "biotoolsID": "proteinsplus", "biotoolsCURIE": "biotools:proteinsplus", "version": [], "otherID": [], "relation": [ { "biotoolsID": "dogsitescorer", "type": "includes" }, { "biotoolsID": "dogsite3", "type": "includes" }, { "biotoolsID": "edia", "type": "includes" }, { "biotoolsID": "siena", "type": "includes" }, { "biotoolsID": "metalizer", "type": "includes" }, { "biotoolsID": "structureprofiler", "type": "includes" }, { "biotoolsID": "jamda", "type": "includes" }, { "biotoolsID": "geomine", "type": "includes" }, { "biotoolsID": "microminer", "type": "includes" }, { "biotoolsID": "poseedit", "type": "includes" }, { "biotoolsID": "poseview", "type": "includes" }, { "biotoolsID": "protoss", "type": "includes" }, { "biotoolsID": "lifesoaks", "type": "includes" }, { "biotoolsID": "ppi", "type": "includes" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0394", "term": "Hydrogen bond calculation" }, { "uri": "http://edamontology.org/operation_0477", "term": "Protein modelling" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1460", "term": "Protein structure" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] }, { "data": { "uri": "http://edamontology.org/data_1461", "term": "Protein-ligand complex" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" }, { "uri": "http://edamontology.org/format_3814", "term": "SDF" } ] }, { "data": { "uri": "http://edamontology.org/data_3021", "term": "UniProt accession" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1463", "term": "Small molecule structure" }, "format": [ { "uri": "http://edamontology.org/format_3814", "term": "SDF" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1460", "term": "Protein structure" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] }, { "data": { "uri": "http://edamontology.org/data_1461", "term": "Protein-ligand complex" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" }, { "uri": "http://edamontology.org/format_3814", "term": "SDF" } ] }, { "data": { "uri": "http://edamontology.org/data_1463", "term": "Small molecule structure" }, "format": [ { "uri": "http://edamontology.org/format_3814", "term": "SDF" } ] } ], "note": "prediction of protonation states and tautomers and placement of hydrogen atoms", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0321", "term": "Protein structure validation" }, { "uri": "http://edamontology.org/operation_2406", "term": "Protein structure analysis" }, { "uri": "http://edamontology.org/operation_3695", "term": "Data filtering" }, { "uri": "http://edamontology.org/operation_1844", "term": "Protein geometry validation" }, { "uri": "http://edamontology.org/operation_0477", "term": "Protein modelling" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1460", "term": "Protein structure" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] }, { "data": { "uri": "http://edamontology.org/data_1461", "term": "Protein-ligand complex" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" }, { "uri": "http://edamontology.org/format_3814", "term": "SDF" } ] }, { "data": { "uri": "http://edamontology.org/data_1463", "term": "Small molecule structure" }, "format": [ { "uri": "http://edamontology.org/format_3814", "term": "SDF" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1539", "term": "Protein structural quality report" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2991", "term": "Protein geometry data" }, "format": [] } ], "note": "quality profiling for protein-ligand complexes", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0570", "term": "Structure visualisation" }, { "uri": "http://edamontology.org/operation_0384", "term": "Accessible surface calculation" }, { "uri": "http://edamontology.org/operation_2480", "term": "Structure analysis" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1460", "term": "Protein structure" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] }, { "data": { "uri": "http://edamontology.org/data_1461", "term": "Protein-ligand complex" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" }, { "uri": "http://edamontology.org/format_3814", "term": "SDF" } ] }, { "data": { "uri": "http://edamontology.org/data_1463", "term": "Small molecule structure" }, "format": [ { "uri": "http://edamontology.org/format_3814", "term": "SDF" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1537", "term": "Protein structure report" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] }, { "data": { "uri": "http://edamontology.org/data_2019", "term": "Map data" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1542", "term": "Protein solvent accessibility" }, "format": [] } ], "note": "calculating bottleneck radii for crystal solvent channels", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0321", "term": "Protein structure validation" }, { "uri": "http://edamontology.org/operation_0570", "term": "Structure visualisation" }, { "uri": "http://edamontology.org/operation_3695", "term": "Data filtering" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1460", "term": "Protein structure" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] }, { "data": { "uri": "http://edamontology.org/data_1461", "term": "Protein-ligand complex" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" }, { "uri": "http://edamontology.org/format_3814", "term": "SDF" } ] }, { "data": { "uri": "http://edamontology.org/data_1463", "term": "Small molecule structure" }, "format": [ { "uri": "http://edamontology.org/format_3814", "term": "SDF" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1460", "term": "Protein structure" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] }, { "data": { "uri": "http://edamontology.org/data_1461", "term": "Protein-ligand complex" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] }, { "data": { "uri": "http://edamontology.org/data_1772", "term": "Score" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1537", "term": "Protein structure report" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] }, { "data": { "uri": "http://edamontology.org/data_2019", "term": "Map data" }, "format": [] } ], "note": "atom-level assessment of the electron density fit for structures solved by X-ray crystallography", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_2949", "term": "Protein-protein interaction analysis" }, { "uri": "http://edamontology.org/operation_2406", "term": "Protein structure analysis" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1460", "term": "Protein structure" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1772", "term": "Score" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1460", "term": "Protein structure" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] } ], "note": "protein-protein interface classification (permanent, transient, crystal artifact)", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0394", "term": "Hydrogen bond calculation" }, { "uri": "http://edamontology.org/operation_1839", "term": "Salt bridge calculation" }, { "uri": "http://edamontology.org/operation_0248", "term": "Residue interaction calculation" }, { "uri": "http://edamontology.org/operation_0482", "term": "Protein-ligand docking" }, { "uri": "http://edamontology.org/operation_1834", "term": "Protein-metal contact calculation" }, { "uri": "http://edamontology.org/operation_0477", "term": "Protein modelling" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1460", "term": "Protein structure" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] }, { "data": { "uri": "http://edamontology.org/data_1461", "term": "Protein-ligand complex" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" }, { "uri": "http://edamontology.org/format_3814", "term": "SDF" } ] }, { "data": { "uri": "http://edamontology.org/data_3021", "term": "UniProt accession" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1463", "term": "Small molecule structure" }, "format": [ { "uri": "http://edamontology.org/format_1197", "term": "InChI" }, { "uri": "http://edamontology.org/format_1196", "term": "SMILES" }, { "uri": "http://edamontology.org/format_3816", "term": "Mol2" }, { "uri": "http://edamontology.org/format_3814", "term": "SDF" } ] }, { "data": { "uri": "http://edamontology.org/data_1463", "term": "Small molecule structure" }, "format": [ { "uri": "http://edamontology.org/format_3814", "term": "SDF" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1537", "term": "Protein structure report" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" } ] }, { "data": { "uri": "http://edamontology.org/data_1461", "term": "Protein-ligand complex" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" }, { "uri": "http://edamontology.org/format_3814", "term": "SDF" } ] }, { "data": { "uri": "http://edamontology.org/data_1772", "term": "Score" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1463", "term": "Small molecule structure" }, "format": [ { "uri": "http://edamontology.org/format_3814", "term": "SDF" } ] }, { "data": { "uri": "http://edamontology.org/data_1460", "term": "Protein structure" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] }, { "data": { "uri": "http://edamontology.org/data_1497", "term": "Root-mean-square deviation" }, "format": [] } ], "note": "protein-ligand docking for small molecules", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_2406", "term": "Protein structure analysis" }, { "uri": "http://edamontology.org/operation_3897", "term": "Ligand-binding site prediction" }, { "uri": "http://edamontology.org/operation_0477", "term": "Protein modelling" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1460", "term": "Protein structure" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] }, { "data": { "uri": "http://edamontology.org/data_1461", "term": "Protein-ligand complex" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" }, { "uri": "http://edamontology.org/format_3814", "term": "SDF" } ] }, { "data": { "uri": "http://edamontology.org/data_3021", "term": "UniProt accession" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1463", "term": "Small molecule structure" }, "format": [ { "uri": "http://edamontology.org/format_3814", "term": "SDF" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1277", "term": "Protein features" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] }, { "data": { "uri": "http://edamontology.org/data_1460", "term": "Protein structure" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] }, { "data": { "uri": "http://edamontology.org/data_1537", "term": "Protein structure report" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] }, { "data": { "uri": "http://edamontology.org/data_2019", "term": "Map data" }, "format": [] } ], "note": "small molecule binding site detection", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_2406", "term": "Protein structure analysis" }, { "uri": "http://edamontology.org/operation_3897", "term": "Ligand-binding site prediction" }, { "uri": "http://edamontology.org/operation_0477", "term": "Protein modelling" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1460", "term": "Protein structure" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] }, { "data": { "uri": "http://edamontology.org/data_1461", "term": "Protein-ligand complex" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" }, { "uri": "http://edamontology.org/format_3814", "term": "SDF" } ] }, { "data": { "uri": "http://edamontology.org/data_3021", "term": "UniProt accession" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1463", "term": "Small molecule structure" }, "format": [ { "uri": "http://edamontology.org/format_3814", "term": "SDF" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1277", "term": "Protein features" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] }, { "data": { "uri": "http://edamontology.org/data_1460", "term": "Protein structure" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] }, { "data": { "uri": "http://edamontology.org/data_1537", "term": "Protein structure report" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] }, { "data": { "uri": "http://edamontology.org/data_1772", "term": "Score" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2019", "term": "Map data" }, "format": [] } ], "note": "small molecule binding site detection and druggability assessment", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0394", "term": "Hydrogen bond calculation" }, { "uri": "http://edamontology.org/operation_0570", "term": "Structure visualisation" }, { "uri": "http://edamontology.org/operation_1839", "term": "Salt bridge calculation" }, { "uri": "http://edamontology.org/operation_0248", "term": "Residue interaction calculation" }, { "uri": "http://edamontology.org/operation_3925", "term": "Network visualisation" }, { "uri": "http://edamontology.org/operation_1834", "term": "Protein-metal contact calculation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1460", "term": "Protein structure" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] }, { "data": { "uri": "http://edamontology.org/data_1461", "term": "Protein-ligand complex" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" }, { "uri": "http://edamontology.org/format_3814", "term": "SDF" } ] }, { "data": { "uri": "http://edamontology.org/data_1463", "term": "Small molecule structure" }, "format": [ { "uri": "http://edamontology.org/format_3814", "term": "SDF" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1566", "term": "Protein-ligand interaction report" }, "format": [ { "uri": "http://edamontology.org/format_3604", "term": "SVG" }, { "uri": "http://edamontology.org/format_2330", "term": "Textual format" }, { "uri": "http://edamontology.org/format_3464", "term": "JSON" } ] }, { "data": { "uri": "http://edamontology.org/data_2992", "term": "Protein structure image" }, "format": [ { "uri": "http://edamontology.org/format_3604", "term": "SVG" }, { "uri": "http://edamontology.org/format_3464", "term": "JSON" } ] }, { "data": { "uri": "http://edamontology.org/data_1712", "term": "Chemical structure image" }, "format": [ { "uri": "http://edamontology.org/format_3604", "term": "SVG" }, { "uri": "http://edamontology.org/format_3464", "term": "JSON" } ] }, { "data": { "uri": "http://edamontology.org/data_0906", "term": "Protein interaction data" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "note": "2D interaction diagram drawing and editing", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_2406", "term": "Protein structure analysis" }, { "uri": "http://edamontology.org/operation_1834", "term": "Protein-metal contact calculation" }, { "uri": "http://edamontology.org/operation_0477", "term": "Protein modelling" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1460", "term": "Protein structure" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] }, { "data": { "uri": "http://edamontology.org/data_1461", "term": "Protein-ligand complex" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" }, { "uri": "http://edamontology.org/format_3814", "term": "SDF" } ] }, { "data": { "uri": "http://edamontology.org/data_1463", "term": "Small molecule structure" }, "format": [ { "uri": "http://edamontology.org/format_3814", "term": "SDF" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0906", "term": "Protein interaction data" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] }, { "data": { "uri": "http://edamontology.org/data_1772", "term": "Score" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1497", "term": "Root-mean-square deviation" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1537", "term": "Protein structure report" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "note": "metal complex geometry prediction", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0570", "term": "Structure visualisation" }, { "uri": "http://edamontology.org/operation_1839", "term": "Salt bridge calculation" }, { "uri": "http://edamontology.org/operation_1834", "term": "Protein-metal contact calculation" }, { "uri": "http://edamontology.org/operation_0248", "term": "Residue interaction calculation" }, { "uri": "http://edamontology.org/operation_3925", "term": "Network visualisation" }, { "uri": "http://edamontology.org/operation_0394", "term": "Hydrogen bond calculation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1460", "term": "Protein structure" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] }, { "data": { "uri": "http://edamontology.org/data_1461", "term": "Protein-ligand complex" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" }, { "uri": "http://edamontology.org/format_3814", "term": "SDF" } ] }, { "data": { "uri": "http://edamontology.org/data_1463", "term": "Small molecule structure" }, "format": [ { "uri": "http://edamontology.org/format_3814", "term": "SDF" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1566", "term": "Protein-ligand interaction report" }, "format": [ { "uri": "http://edamontology.org/format_3508", "term": "PDF" }, { "uri": "http://edamontology.org/format_3604", "term": "SVG" }, { "uri": "http://edamontology.org/format_3603", "term": "PNG" } ] }, { "data": { "uri": "http://edamontology.org/data_1712", "term": "Chemical structure image" }, "format": [ { "uri": "http://edamontology.org/format_3508", "term": "PDF" }, { "uri": "http://edamontology.org/format_3604", "term": "SVG" }, { "uri": "http://edamontology.org/format_3603", "term": "PNG" } ] }, { "data": { "uri": "http://edamontology.org/data_2992", "term": "Protein structure image" }, "format": [ { "uri": "http://edamontology.org/format_3508", "term": "PDF" }, { "uri": "http://edamontology.org/format_3604", "term": "SVG" }, { "uri": "http://edamontology.org/format_3603", "term": "PNG" } ] } ], "note": "2D interaction diagram drawing", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0339", "term": "Structure database search" }, { "uri": "http://edamontology.org/operation_0503", "term": "Pairwise structure alignment" }, { "uri": "http://edamontology.org/operation_0509", "term": "Local structure alignment" }, { "uri": "http://edamontology.org/operation_0360", "term": "Structural similarity search" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1460", "term": "Protein structure" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] }, { "data": { "uri": "http://edamontology.org/data_3021", "term": "UniProt accession" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1461", "term": "Protein-ligand complex" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" }, { "uri": "http://edamontology.org/format_3814", "term": "SDF" } ] }, { "data": { "uri": "http://edamontology.org/data_1463", "term": "Small molecule structure" }, "format": [ { "uri": "http://edamontology.org/format_3814", "term": "SDF" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1497", "term": "Root-mean-square deviation" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1481", "term": "Protein structure alignment" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] }, { "data": { "uri": "http://edamontology.org/data_1460", "term": "Protein structure" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] }, { "data": { "uri": "http://edamontology.org/data_2080", "term": "Database search results" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "note": "structural single-residue substitution search and analysis", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_2844", "term": "Structure clustering" }, { "uri": "http://edamontology.org/operation_0244", "term": "Simulation analysis" }, { "uri": "http://edamontology.org/operation_0360", "term": "Structural similarity search" }, { "uri": "http://edamontology.org/operation_0339", "term": "Structure database search" }, { "uri": "http://edamontology.org/operation_0509", "term": "Local structure alignment" }, { "uri": "http://edamontology.org/operation_0503", "term": "Pairwise structure alignment" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1460", "term": "Protein structure" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] }, { "data": { "uri": "http://edamontology.org/data_1461", "term": "Protein-ligand complex" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" }, { "uri": "http://edamontology.org/format_3814", "term": "SDF" } ] }, { "data": { "uri": "http://edamontology.org/data_3021", "term": "UniProt accession" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1463", "term": "Small molecule structure" }, "format": [ { "uri": "http://edamontology.org/format_3814", "term": "SDF" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1460", "term": "Protein structure" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] }, { "data": { "uri": "http://edamontology.org/data_1384", "term": "Sequence alignment (protein)" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1497", "term": "Root-mean-square deviation" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1463", "term": "Small molecule structure" }, "format": [ { "uri": "http://edamontology.org/format_3814", "term": "SDF" } ] }, { "data": { "uri": "http://edamontology.org/data_1481", "term": "Protein structure alignment" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] }, { "data": { "uri": "http://edamontology.org/data_2080", "term": "Database search results" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "note": "PDB mining and protein binding site ensemble generation", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0244", "term": "Simulation analysis" }, { "uri": "http://edamontology.org/operation_0306", "term": "Text mining" }, { "uri": "http://edamontology.org/operation_0360", "term": "Structural similarity search" }, { "uri": "http://edamontology.org/operation_0339", "term": "Structure database search" }, { "uri": "http://edamontology.org/operation_0509", "term": "Local structure alignment" }, { "uri": "http://edamontology.org/operation_0503", "term": "Pairwise structure alignment" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1460", "term": "Protein structure" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] }, { "data": { "uri": "http://edamontology.org/data_1461", "term": "Protein-ligand complex" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" }, { "uri": "http://edamontology.org/format_3814", "term": "SDF" } ] }, { "data": { "uri": "http://edamontology.org/data_3021", "term": "UniProt accession" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1463", "term": "Small molecule structure" }, "format": [ { "uri": "http://edamontology.org/format_3814", "term": "SDF" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2080", "term": "Database search results" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] }, { "data": { "uri": "http://edamontology.org/data_1481", "term": "Protein structure alignment" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] }, { "data": { "uri": "http://edamontology.org/data_1460", "term": "Protein structure" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] }, { "data": { "uri": "http://edamontology.org/data_1497", "term": "Root-mean-square deviation" }, "format": [] } ], "note": "textual, numerical, and chemical 3D searches in the PDB", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0394", "term": "Hydrogen bond calculation" }, { "uri": "http://edamontology.org/operation_0477", "term": "Protein modelling" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1461", "term": "Protein-ligand complex" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" }, { "uri": "http://edamontology.org/format_3814", "term": "SDF" } ] }, { "data": { "uri": "http://edamontology.org/data_1463", "term": "Small molecule structure" }, "format": [ { "uri": "http://edamontology.org/format_3814", "term": "SDF" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1460", "term": "Protein structure" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] }, { "data": { "uri": "http://edamontology.org/data_1537", "term": "Protein structure report" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "note": "water molecule placement", "cmd": null } ], "toolType": [ "Web service", "Web API" ], "topic": [ { "uri": "http://edamontology.org/topic_0081", "term": "Structure analysis" }, { "uri": "http://edamontology.org/topic_3534", "term": "Protein binding sites" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": "Other", "collectionID": [ "de.NBI", "de.NBI-biodata" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": null, "elixirPlatform": [ "Tools" ], "elixirNode": [ "Germany" ], "elixirCommunity": [ "3D-BioInfo" ], "link": [ { "url": "https://proteins.plus", "type": [ "Service" ], "note": null } ], "download": [], "documentation": [ { "url": "https://proteins.plus/help/index", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gkx333", "pmid": "28472372", "pmcid": "PMC5570178", "type": [ "Primary" ], "version": null, "note": null, "metadata": null }, { "doi": "10.1093/nar/gkaa235", "pmid": "32297936", "pmcid": "PMC7319454", "type": [ "Usage" ], "version": null, "note": null, "metadata": null }, { "doi": "10.1093/nar/gkac305", "pmid": "35489057", "pmcid": "PMC9252762", "type": [ "Usage" ], "version": null, "note": null, "metadata": null }, { "doi": "10.1093/nar/gkaf377", "pmid": "40326518", "pmcid": "PMC12230695", "type": [ "Usage" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "ProteinsPlus Support", "email": "proteinsplus.zbh@lists.uni-hamburg.de", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Primary contact" ], "note": "Primary Contact for Web Service Issues" }, { "name": "University of Hamburg, ZBH - Center for Bioinformatics", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": "00g30e956", "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null } ], "owner": "ehrt", "additionDate": "2017-08-01T11:05:01Z", "lastUpdate": "2026-06-12T09:56:30.953754Z", "editPermission": { "type": "group", "authors": [ "MelanieZBH", "ehrt" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "SIENA", "description": "SIENA is a software pipeline enabling the fully automated construction of protein structure ensembles from the PDB. Starting with a single query structure, all binding sites with high sequence similarity are extracted from the PDB, aligned, and superimposed. SIENA also handles complicated cases, such as comparing binding sites at protein domain interfaces or within multimeric proteins.", "homepage": "https://www.zbh.uni-hamburg.de/en/forschung/amd/software/siena.html", "biotoolsID": "siena", "biotoolsCURIE": "biotools:siena", "version": [], "otherID": [], "relation": [ { "biotoolsID": "proteinsplus", "type": "includedIn" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2844", "term": "Structure clustering" }, { "uri": "http://edamontology.org/operation_0244", "term": "Simulation analysis" }, { "uri": "http://edamontology.org/operation_0360", "term": "Structural similarity search" }, { "uri": "http://edamontology.org/operation_0339", "term": "Structure database search" }, { "uri": "http://edamontology.org/operation_0509", "term": "Local structure alignment" }, { "uri": "http://edamontology.org/operation_0503", "term": "Pairwise structure alignment" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1460", "term": "Protein structure" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] }, { "data": { "uri": "http://edamontology.org/data_1461", "term": "Protein-ligand complex" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" }, { "uri": "http://edamontology.org/format_3814", "term": "SDF" } ] }, { "data": { "uri": "http://edamontology.org/data_3021", "term": "UniProt accession" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1463", "term": "Small molecule structure" }, "format": [ { "uri": "http://edamontology.org/format_3814", "term": "SDF" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1460", "term": "Protein structure" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] }, { "data": { "uri": "http://edamontology.org/data_1384", "term": "Sequence alignment (protein)" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1497", "term": "Root-mean-square deviation" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1463", "term": "Small molecule structure" }, "format": [ { "uri": "http://edamontology.org/format_3814", "term": "SDF" } ] }, { "data": { "uri": "http://edamontology.org/data_1481", "term": "Protein structure alignment" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] }, { "data": { "uri": "http://edamontology.org/data_2080", "term": "Database search results" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "note": "PDB mining and protein binding site ensemble generation", "cmd": null } ], "toolType": [ "Web service", "Web API", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3534", "term": "Protein binding sites" }, { "uri": "http://edamontology.org/topic_3336", "term": "Drug discovery" }, { "uri": "http://edamontology.org/topic_3473", "term": "Data mining" }, { "uri": "http://edamontology.org/topic_2814", "term": "Protein structure analysis" }, { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" }, { "uri": "http://edamontology.org/topic_0128", "term": "Protein interactions" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": "Other", "collectionID": [ "de.NBI", "de.NBI-biodata" ], "maturity": "Mature", "cost": "Free of charge (with restrictions)", "accessibility": null, "elixirPlatform": [ "Tools" ], "elixirNode": [ "Germany" ], "elixirCommunity": [ "3D-BioInfo" ], "link": [ { "url": "https://proteins.plus", "type": [ "Service" ], "note": "A web service to run SIENA calculations for protein structures stored in the Protein Data Bank and AlphaFold Protein Structure Database or uploaded structures." }, { "url": "https://proteins.plus/help/siena_rest", "type": [ "Service" ], "note": "A web API to run SIENA calculations for protein structures stored in the Protein Data Bank and AlphaFold Protein Structure Database or uploaded structures." }, { "url": "https://uhh.de/naomi", "type": [ "Software catalogue" ], "note": "A link to download the standalone tool from the NAOMI ChemBio Suite." } ], "download": [ { "url": "https://uhh.de/naomi", "type": "Binaries", "note": "Please register to download the tool.", "version": null } ], "documentation": [ { "url": "https://proteins.plus/help/index", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1021/acs.jcim.5b00588", "pmid": "26759067", "pmcid": null, "type": [ "Method", "Primary" ], "version": null, "note": null, "metadata": null }, { "doi": "10.1021/acs.jcim.5b00210", "pmid": "26098831", "pmcid": null, "type": [ "Method" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "ProteinsPlus Support", "email": "proteinsplus.zbh@lists.uni-hamburg.de", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Primary contact" ], "note": "Primary Contact for Web Service Issues" }, { "name": "NAOMI ChemBio Suite Support", "email": "software.zbh@uni-hamburg.de", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Primary contact" ], "note": "Primary Contact for Standalone Tool Issues" }, { "name": "University of Hamburg, ZBH - Center for Bioinformatics", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": "00g30e956", "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null } ], "owner": "ehrt", "additionDate": "2016-11-28T10:07:17Z", "lastUpdate": "2026-06-12T08:59:19.128862Z", "editPermission": { "type": "group", "authors": [ "ehrt", "MelanieZBH" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "SPALN", "description": "Genome mapping and spliced alignment of cDNA or amino acid sequences", "homepage": "https://github.com/ogotoh/spaln", "biotoolsID": "spaln", "biotoolsCURIE": "biotools:spaln", "version": [ "ver.3.0.8b" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2429", "term": "Mapping" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2977", "term": "Nucleic acid sequence" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2976", "term": "Protein sequence" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1234", "term": "Sequence set (nucleic acid)" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0102", "term": "Mapping" } ], "operatingSystem": [], "language": [ "C", "Perl", "C++" ], "license": "GPL-2.0", "collectionID": [], "maturity": "Mature", "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/ogotoh/spaln", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [ { "url": "https://github.com/ogotoh/spaln", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gkag357", "pmid": "42134803", "pmcid": "PMC13175633", "type": [], "version": null, "note": null, "metadata": null }, { "doi": "10.1093/bioinformatics/btn460", "pmid": "18728043", "pmcid": null, "type": [], "version": null, "note": null, "metadata": null }, { "doi": "10.1093/nar/gks708", "pmid": "22848105", "pmcid": "PMC3488211", "type": [], "version": null, "note": null, "metadata": null }, { "doi": "10.1093/bioinformatics/16.3.190", "pmid": "10869012", "pmcid": null, "type": [], "version": null, "note": null, "metadata": null }, { "doi": "10.1093/bioinformatics/btae517", "pmid": "39152995", "pmcid": "PMC11361809", "type": [], "version": null, "note": null, "metadata": null }, { "doi": "10.1007/978-1-0716-1036-7_5", "pmid": "33289887", "pmcid": null, "type": [], "version": null, "note": null, "metadata": null }, { "doi": "10.1093/bioinformatics/btl067", "pmid": "16500940", "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Osamu Gotoh", "email": "gotoh.osamu.67a@st.kyoto-u.ac.jp", "url": null, "orcidid": "https://orcid.org/0009-0002-6750-1945", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "owner": "aniehues", "additionDate": "2026-06-04T08:27:22.148216Z", "lastUpdate": "2026-06-04T08:27:22.150479Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "VerityMap", "description": "VerityMap is a tool for mapping long reads to assemblies of extra-long tandem repeats, producing SAM files and identifying potential heterozygous sites and assembly errors through analysis of rare k-mers. It supports PacBio HiFi and ONT reads and generates interactive HTML plots for variant analysis.", "homepage": "https://github.com/ablab/VerityMap", "biotoolsID": "VerityMap", "biotoolsCURIE": "biotools:VerityMap", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0523", "term": "Mapping assembly" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3494", "term": "DNA sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_2572", "term": "BAM" }, { "uri": "http://edamontology.org/format_3003", "term": "BED" } ] } ], "note": null, "cmd": null } ], "toolType": [], "topic": [ { "uri": "http://edamontology.org/topic_0102", "term": "Mapping" }, { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" } ], "operatingSystem": [], "language": [ "C", "CUDA", "Python", "C++" ], "license": "GPL-3.0", "collectionID": [], "maturity": "Mature", "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/ablab/tandemQUAST/issues", "type": [ "Issue tracker" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1093/bioinformatics/btaa440", "pmid": "32657355", "pmcid": "PMC7355294", "type": [], "version": null, "note": null, "metadata": null } ], "credit": [], "owner": "n.m.palmblad@lumc.nl", "additionDate": "2026-06-04T08:25:03.738887Z", "lastUpdate": "2026-06-04T08:25:03.740814Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "SNP-sites", "description": "Finds SNP sites from a multi-FASTA alignment file.", "homepage": "https://sanger-pathogens.github.io/snp-sites/", "biotoolsID": "snp-sites", "biotoolsCURIE": "biotools:snp-sites", "version": [ "2.5.1" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0484", "term": "SNP detection" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1383", "term": "Nucleic acid sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_3820", "term": "Relaxed PHYLIP Sequential" }, { "uri": "http://edamontology.org/format_1984", "term": "FASTA-aln" }, { "uri": "http://edamontology.org/format_3016", "term": "VCF" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1383", "term": "Nucleic acid sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_3820", "term": "Relaxed PHYLIP Sequential" }, { "uri": "http://edamontology.org/format_1984", "term": "FASTA-aln" }, { "uri": "http://edamontology.org/format_3016", "term": "VCF" } ] } ], "note": null, "cmd": "snp-sites my_alignment.aln\nsnp-sites my_gzipped_alignment.aln.gz" } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" }, { "uri": "http://edamontology.org/topic_2885", "term": "DNA polymorphism" } ], "operatingSystem": [ "Linux" ], "language": [ "C" ], "license": "GPL-3.0", "collectionID": [], "maturity": null, "cost": null, "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/sanger-pathogens/snp-sites", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [ { "url": "https://sanger-pathogens.github.io/snp-sites/", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1099/mgen.0.000056", "pmid": "28348851", "pmcid": "PMC5320690", "type": [ "Primary" ], "version": null, "note": null, "metadata": null } ], "credit": [], "owner": "aniehues", "additionDate": "2026-05-20T08:59:02.212508Z", "lastUpdate": "2026-05-20T08:59:02.214591Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "sam2interval", "description": "A Python script that converts positional information from a SAM dataset into interval format with 0-based start and 1-based end. CIGAR string of SAM format is used to compute the end coordinate.", "homepage": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/sam2interval", "biotoolsID": "sam2interval", "biotoolsCURIE": "biotools:sam2interval", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3434", "term": "Conversion" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_2573", "term": "SAM" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_2572", "term": "BAM" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Script" ], "topic": [ { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" } ], "operatingSystem": [ "Mac", "Windows", "Linux" ], "language": [ "Python" ], "license": "MIT", "collectionID": [], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [ "Galaxy" ], "link": [ { "url": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/sam2interval", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [], "publication": [], "credit": [], "owner": "VKasalica", "additionDate": "2026-05-19T23:23:06.270637Z", "lastUpdate": "2026-05-19T23:35:39.572272Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "RepeatAfterMe", "description": "RepeatAfterMe is a package for the extension of repetitive DNA cores. The tool automatically extends a multiple sequence alignment that may represent only a fragment of a longer repetitive sequence family.", "homepage": "https://github.com/Dfam-consortium/RepeatAfterMe", "biotoolsID": "repeatafterme", "biotoolsCURIE": "biotools:repeatafterme", "version": [ "v0.0.7" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0495", "term": "Local alignment" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3494", "term": "DNA sequence" }, "format": [ { "uri": "http://edamontology.org/format_3009", "term": "2bit" } ] }, { "data": { "uri": "http://edamontology.org/data_1017", "term": "Sequence range" }, "format": [ { "uri": "http://edamontology.org/format_3585", "term": "bed6" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "note": null, "cmd": "./RAMExtend -ranges test/extension-test2.tsv -twobit test/extension-test2.2bit" } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" } ], "operatingSystem": [ "Mac", "Linux" ], "language": [ "C" ], "license": "CC0-1.0", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [ { "name": "Robert Hubley", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null } ], "owner": "Pub2Tools", "additionDate": "2026-05-08T10:33:02.567199Z", "lastUpdate": "2026-05-08T10:33:02.569259Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "slow5-dorado", "description": "Fork of dorado (high-performance, easy-to-use, open source analysis engine for Oxford Nanopore reads) that support S/BLOW5", "homepage": "https://github.com/hiruna72/slow5-dorado", "biotoolsID": "slow5-dorado", "biotoolsCURIE": "biotools:slow5-dorado", "version": [ "1.1.1" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3185", "term": "Base-calling" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0924", "term": "Sequence trace" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1383", "term": "Nucleic acid sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_2572", "term": "BAM" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_4056", "term": "Long-read sequencing" }, { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" } ], "operatingSystem": [ "Linux" ], "language": [ "C++" ], "license": "Other", "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "owner": "veitveit11", "additionDate": "2026-05-05T06:03:45.867892Z", "lastUpdate": "2026-05-05T06:03:45.870767Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "bwa-meth", "description": "bwa-meth is a tool for alignment of Bisulfite sequencing reads.", "homepage": "https://github.com/brentp/bwa-meth", "biotoolsID": "bwa-meth", "biotoolsCURIE": "biotools:bwa-meth", "version": [ "0.2.9" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0292", "term": "Sequence alignment" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2977", "term": "Nucleic acid sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_2977", "term": "Nucleic acid sequence" }, "format": [ { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" } ] }, { "data": { "uri": "http://edamontology.org/data_2977", "term": "Nucleic acid sequence" }, "format": [ { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1383", "term": "Nucleic acid sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_2573", "term": "SAM" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0102", "term": "Mapping" }, { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" } ], "operatingSystem": [ "Linux" ], "language": [ "Python" ], "license": "MIT", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.48550/arXiv.1401.1129", "pmid": null, "pmcid": null, "type": [ "Preprint" ], "version": null, "note": null, "metadata": null } ], "credit": [], "owner": "n.m.palmblad@lumc.nl", "additionDate": "2026-05-01T10:45:51.114755Z", "lastUpdate": "2026-05-01T10:45:51.117070Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "PLAST", "description": "PLAST is a heuristical method to search for highest scoring local alignments between a DNA sequence query and a graphical pangenome. It takes as input a plain DNA sequence and a pangenome which may either be a set of (multiple) FASTA or FASTQ files or a sequence graph constructed by the tool Bifrost. It then outputs statistically meaningful (gapped) alignments in the style of the NCBI BLAST standard output format. Alignments are calculated based on a \"seed-and-extend approach\" while traversing the sequence graph. Biologically meaningful alignments are filtered by using an alignment statistic explicitly developed for sequence-to-graph alignments involving graphical pangenomes.", "homepage": "https://github.com/tischulz1/plast", "biotoolsID": "pangenome-blast", "biotoolsCURIE": "biotools:pangenome-blast", "version": [ "0.0.1-0.2.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0495", "term": "Local alignment" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3494", "term": "DNA sequence" }, "format": [ { "uri": "http://edamontology.org/format_1211", "term": "unambiguous pure nucleotide" } ] }, { "data": { "uri": "http://edamontology.org/data_1234", "term": "Sequence set (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_3975", "term": "GFA 1" }, { "uri": "http://edamontology.org/format_2333", "term": "Binary format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1383", "term": "Nucleic acid sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_1333", "term": "BLAST results" } ] } ], "note": "In order to search for alignments within the pangenome graph, \nA pangenome graph used to search for alignments consists of (1) a file in GFA format containing all sequences of the graph, (2) a binary file produced by the tool itself or the software \"Bifrost\" and (3) a program-specific index data structure in binary format.", "cmd": "PLAST Search -i pangenomeGraphCommonFilePrefix -q fileContainingOneQueryPerLine" }, { "operation": [ { "uri": "http://edamontology.org/operation_0227", "term": "Indexing" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0850", "term": "Sequence set" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" }, { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0850", "term": "Sequence set" }, "format": [ { "uri": "http://edamontology.org/format_3975", "term": "GFA 1" }, { "uri": "http://edamontology.org/format_2333", "term": "Binary format" } ] } ], "note": "If a pangenome graph already exists and only an index has to be built, FASTA/FASTQ files are not needed.", "cmd": "PLAST Build -i pangenomeGraphCommonFilePrefix -R *.fasta" } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0797", "term": "Comparative genomics" }, { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" } ], "operatingSystem": [ "Linux", "Mac", "Windows" ], "language": [ "C++" ], "license": "GPL-3.0", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://gitlab.ub.uni-bielefeld.de/gi/plast", "type": [ "Repository" ], "note": null }, { "url": "https://github.com/tischulz1/plast", "type": [ "Mirror" ], "note": null } ], "download": [], "documentation": [ { "url": "https://gitlab.ub.uni-bielefeld.de/gi/plast/-/blob/master/README.md", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btab077", "pmid": "33532821", "pmcid": "PMC8388040", "type": [ "Primary", "Method", "Benchmarking study" ], "version": null, "note": null, "metadata": { "title": "Detecting high-scoring local alignments in pangenome graphs", "abstract": "Motivation: Increasing amounts of individual genomes sequenced per species motivate the usage of pangenomic approaches. Pangenomes may be represented as graphical structures, e.g. compacted colored de Bruijn graphs, which offer a low memory usage and facilitate reference-free sequence comparisons. While sequence-to-graph mapping to graphical pangenomes has been studied for some time, no local alignment search tool in the vein of BLAST has been proposed yet. Results: We present a new heuristic method to find maximum scoring local alignments of a DNA query sequence to a pangenome represented as a compacted colored de Bruijn graph. Our approach additionally allows a comparison of similarity among sequences within the pangenome. We show that local alignment scores follow an exponential-tail distribution similar to BLAST scores, and we discuss how to estimate its parameters to separate local alignments representing sequence homology from spurious findings. An implementation of our method is presented, and its performance and usability are shown. Our approach scales sublinearly in running time and memory usage with respect to the number of genomes under consideration. This is an advantage over classical methods that do not make use of sequence similarity within the pangenome.", "date": "2021-08-15T00:00:00Z", "citationCount": 6, "authors": [ { "name": "Schulz T." }, { "name": "Wittler R." }, { "name": "Rahmann S." }, { "name": "Hach F." }, { "name": "Stoye J." } ], "journal": "Bioinformatics" } } ], "credit": [ { "name": "Bielefeld University", "email": null, "url": "https://www.uni-bielefeld.de/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Genome Informatics", "email": null, "url": "https://gi.cebitec.uni-bielefeld.de/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Tizian Schulz", "email": "plast-service@cebitec.uni-bielefeld.de", "url": null, "orcidid": "https://orcid.org/0000-0003-0744-7078", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null } ], "owner": "tizian", "additionDate": "2021-05-06T06:18:52Z", "lastUpdate": "2026-02-26T11:22:02.485629Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "BioMaS (Bioinformatic analysis of Metagenomic amplicons)", "description": "BioMaS is a friendly pipeline for Meta-barcoding HTS data analysis specifically designed for users without particular computing skills.", "homepage": "http://itsonewb.cloud.ba.infn.it/galaxy/tool_runner?tool_id=biomas2_wrapper", "biotoolsID": "biomas_bioinformatic_analysis_of_metagenomic_amplicons", "biotoolsCURIE": "biotools:biomas_bioinformatic_analysis_of_metagenomic_amplicons", "version": [ "1.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3460", "term": "Taxonomic classification" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1383", "term": "Nucleic acid sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_2573", "term": "SAM" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3028", "term": "Taxonomy" }, "format": [ { "uri": "http://edamontology.org/format_1910", "term": "newick" } ] } ], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0232", "term": "Sequence merging" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3494", "term": "DNA sequence" }, "format": [ { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3494", "term": "DNA sequence" }, "format": [ { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" } ] } ], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0496", "term": "Global alignment" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3494", "term": "DNA sequence" }, "format": [ { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1383", "term": "Nucleic acid sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_2573", "term": "SAM" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_3391", "term": "Omics" } ], "operatingSystem": [ "Linux", "Mac", "Windows" ], "language": [ "Bash", "Python" ], "license": "Not licensed", "collectionID": [], "maturity": "Emerging", "cost": "Free of charge (with restrictions)", "accessibility": "Open access (with restrictions)", "elixirPlatform": [ "Tools" ], "elixirNode": [ "Italy" ], "elixirCommunity": [ "Marine Metagenomics" ], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.1186/s12859-015-0595-z", "pmid": "26130132", "pmcid": "PMC4486701", "type": [ "Method" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Bruno Fosso", "email": "b.fosso@ibiom.cnr.it", "url": null, "orcidid": "https://orcid.org/0000-0003-2324-086X", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": "Researcher at CNR-IBIOM" }, { "name": "Graziano Pesole", "email": "graziano.pesole@uniba.it", "url": null, "orcidid": "https://orcid.org/0000-0003-3663-0859", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": "Full Professor of Molecular Biology at University of Bari" }, { "name": "Monica Santamaria", "email": "m.santamaria@ibiom.cnr.it", "url": null, "orcidid": "https://orcid.org/0000-0003-1488-6052", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": "Researcher at CNR-IBIOM" } ], "owner": "bfosso", "additionDate": "2021-03-31T15:26:55Z", "lastUpdate": "2026-01-27T17:22:28.785300Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "D-GENIES", "description": "D-GENIES – for Dot plot large Genomes in an Interactive, Efficient and Simple way – is an online tool designed to compare two genomes. It supports large genome and you can interact with the dot plot to improve the visualization.", "homepage": "https://dgenies.toulouse.inrae.fr/", "biotoolsID": "d-genies", "biotoolsCURIE": "biotools:d-genies", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3182", "term": "Genome alignment" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3494", "term": "DNA sequence" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_3494", "term": "DNA sequence" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1383", "term": "Nucleic acid sequence alignment" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2161", "term": "Sequence similarity plot" }, "format": [] } ], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0490", "term": "Dot plot plotting" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1383", "term": "Nucleic acid sequence alignment" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2161", "term": "Sequence similarity plot" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Web application", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" }, { "uri": "http://edamontology.org/topic_0092", "term": "Data visualisation" }, { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" } ], "operatingSystem": [ "Mac", "Linux" ], "language": [ "Python", "Shell" ], "license": "GPL-3.0", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/genotoul-bioinfo/dgenies", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [ { "url": "https://dgenies.readthedocs.io/en/latest/index.html", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.7717/peerj.4958", "pmid": "29888139", "pmcid": "PMC5991294", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "D-GENIES: Dot plot large genomes in an interactive, efficient and simple way", "abstract": "", "date": "2018-01-01T00:00:00Z", "citationCount": 493, "authors": [], "journal": "PeerJ" } } ], "credit": [ { "name": "Floréal Cabanettes", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Christophe Klopp", "email": "christophe.klopp@inrae.fr", "url": null, "orcidid": "https://orcid.org/0000-0001-7126-5477", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Philippe Bordron", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0003-1975-0920", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer" ], "note": null }, { "name": "Vincent Dominguez", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Developer" ], "note": null }, { "name": "GenoToul bioinformatics facility", "email": null, "url": "http://bioinfo.genotoul.fr/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Division", "typeRole": [ "Provider" ], "note": null } ], "owner": "d.gabrielaitis", "additionDate": "2018-07-29T10:31:55Z", "lastUpdate": "2025-12-18T10:02:18.098079Z", "editPermission": { "type": "group", "authors": [ "pbordron" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Jalview", "description": "Jalview is a free cross-platform program for multiple sequence alignment editing, visualisation and analysis. Use it to align, view and edit sequence alignments, analyse them with phylogenetic trees and principal components analysis (PCA) plots and explore molecular structures and annotation.", "homepage": "https://www.jalview.org/", "biotoolsID": "Jalview", "biotoolsCURIE": "biotools:Jalview", "version": [ "2.11.5.1" ], "otherID": [], "relation": [ { "biotoolsID": "jabaws", "type": "uses" }, { "biotoolsID": "chimera", "type": "uses" }, { "biotoolsID": "chimerax", "type": "uses" }, { "biotoolsID": "pymol", "type": "uses" }, { "biotoolsID": "bioconda", "type": "includedIn" }, { "biotoolsID": "3d-beacons", "type": "uses" }, { "biotoolsID": "uniprot", "type": "uses" }, { "biotoolsID": "pfam", "type": "uses" }, { "biotoolsID": "ensembl", "type": "uses" }, { "biotoolsID": "pdb", "type": "uses" }, { "biotoolsID": "rfam", "type": "uses" }, { "biotoolsID": "3d-beacons", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3081", "term": "Sequence alignment editing" }, { "uri": "http://edamontology.org/operation_0324", "term": "Phylogenetic tree analysis" }, { "uri": "http://edamontology.org/operation_0564", "term": "Sequence visualisation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_1948", "term": "nbrf/pir" }, { "uri": "http://edamontology.org/format_1929", "term": "FASTA" }, { "uri": "http://edamontology.org/format_1984", "term": "FASTA-aln" }, { "uri": "http://edamontology.org/format_3015", "term": "Pileup" }, { "uri": "http://edamontology.org/format_1938", "term": "GFF2-seq" }, { "uri": "http://edamontology.org/format_3313", "term": "BLC" }, { "uri": "http://edamontology.org/format_3311", "term": "RNAML" }, { "uri": "http://edamontology.org/format_1915", "term": "Format" }, { "uri": "http://edamontology.org/format_3774", "term": "BioJSON (Jalview)" }, { "uri": "http://edamontology.org/format_1982", "term": "ClustalW format" }, { "uri": "http://edamontology.org/format_1477", "term": "mmCIF" }, { "uri": "http://edamontology.org/format_1997", "term": "PHYLIP format" }, { "uri": "http://edamontology.org/format_3016", "term": "VCF" }, { "uri": "http://edamontology.org/format_1961", "term": "Stockholm format" }, { "uri": "http://edamontology.org/format_1939", "term": "GFF3-seq" }, { "uri": "http://edamontology.org/format_1947", "term": "GCG MSF" } ] }, { "data": { "uri": "http://edamontology.org/data_0886", "term": "Structure alignment" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_1948", "term": "nbrf/pir" }, { "uri": "http://edamontology.org/format_1929", "term": "FASTA" }, { "uri": "http://edamontology.org/format_3015", "term": "Pileup" }, { "uri": "http://edamontology.org/format_3313", "term": "BLC" }, { "uri": "http://edamontology.org/format_3774", "term": "BioJSON (Jalview)" }, { "uri": "http://edamontology.org/format_1982", "term": "ClustalW format" }, { "uri": "http://edamontology.org/format_3464", "term": "JSON" }, { "uri": "http://edamontology.org/format_1997", "term": "PHYLIP format" }, { "uri": "http://edamontology.org/format_1961", "term": "Stockholm format" }, { "uri": "http://edamontology.org/format_1947", "term": "GCG MSF" } ] }, { "data": { "uri": "http://edamontology.org/data_2884", "term": "Plot" }, "format": [ { "uri": "http://edamontology.org/format_3466", "term": "EPS" }, { "uri": "http://edamontology.org/format_1915", "term": "Format" }, { "uri": "http://edamontology.org/format_2331", "term": "HTML" }, { "uri": "http://edamontology.org/format_3604", "term": "SVG" }, { "uri": "http://edamontology.org/format_3603", "term": "PNG" } ] } ], "note": "Other Input formats:\nAMSA (.amsa);\nJnetFile (.concise, .jnet);\nPFAM (.pfam);\nSubstitution matrix (.matrix);\nJalview Project File (.jvp);\nJalview Feature File (.features, .jvfeatures);\nJalview Annotations File (.annotations, .jvannotations);\nPredicted Aligned Error (PAE) Matrix File (.json)\n...\nOther Output formats:\nPFAM (.pfam);\nBioJS (.biojs) (interactive HTML/Javascript);\nJalview Project File (.jvp);", "cmd": null } ], "toolType": [ "Desktop application", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/topic_0092", "term": "Data visualisation" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [], "license": "GPL-3.0", "collectionID": [ "ELIXIR-UK" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [ "Tools", "Interoperability" ], "elixirNode": [ "UK" ], "elixirCommunity": [], "link": [ { "url": "https://discourse.jalview.org/", "type": [ "Discussion forum" ], "note": null }, { "url": "https://issues.jalview.org/", "type": [ "Issue tracker" ], "note": null }, { "url": "https://www.jalview.org/development/jalview_develop/", "type": [ "Other" ], "note": "Latest development version" }, { "url": "https://gitlab.jalview.org/jalview/jalview.git", "type": [ "Repository" ], "note": null }, { "url": "https://twitter.com/Jalview", "type": [ "Social media" ], "note": "Twitter feed" }, { "url": "https://www.youtube.com/channel/UCIjpnvZB770yz7ftbrJ0tfw", "type": [ "Social media" ], "note": "YouTube training videos" }, { "url": "https://www.linkedin.com/company/104771886/", "type": [ "Social media" ], "note": null } ], "download": [ { "url": "https://www.jalview.org/download", "type": "Downloads page", "note": null, "version": null }, { "url": "https://www.jalview.org/download/source/", "type": "Source code", "note": null, "version": null }, { "url": "https://www.jalview.org/download/?os=all", "type": "Binaries", "note": "Binaries for all platforms", "version": null }, { "url": "https://www.jalview.org/favicon.svg", "type": "Icon", "note": null, "version": null }, { "url": "https://www.jalview.org/download/other/jar/", "type": "Binaries", "note": "Executable JAR file", "version": null } ], "documentation": [ { "url": "https://www.jalview.org/about/citation", "type": [ "Citation instructions" ], "note": null }, { "url": "https://www.jalview.org/training/", "type": [ "Training material" ], "note": "Hands-on exercises, Training courses and Training videos" }, { "url": "https://www.jalview.org/help/faq", "type": [ "FAQ" ], "note": null }, { "url": "https://www.jalview.org/help/documentation/", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btp033", "pmid": "19151095", "pmcid": "PMC2672624", "type": [], "version": null, "note": null, "metadata": { "title": "Jalview Version 2-A multiple sequence alignment editor and analysis workbench", "abstract": "", "date": "2009-05-07T00:00:00Z", "citationCount": 7717, "authors": [], "journal": "Bioinformatics" } } ], "credit": [ { "name": "Jim Procter", "email": null, "url": "http://www.lifesci.dundee.ac.uk/people/jim-procter", "orcidid": "https://orcid.org/0000-0002-7865-7382", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Geoff Barton", "email": null, "url": "https://www.lifesci.dundee.ac.uk/people/geoff-barton", "orcidid": "https://orcid.org/0000-0002-9014-5355", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "ben_s", "additionDate": "2019-02-13T17:01:40Z", "lastUpdate": "2025-12-11T14:16:30.074724Z", "editPermission": { "type": "group", "authors": [ "ben_s", "jimprocter" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "SILVA rRNA database", "description": "SILVA provides comprehensive, quality checked and regularly updated datasets of aligned small (16S/18S, SSU) and large subunit (23S/28S, LSU) ribosomal RNA (rRNA) sequences for all three domains of life (Bacteria, Archaea and Eukaryota).", "homepage": "https://www.arb-silva.de", "biotoolsID": "silva", "biotoolsCURIE": "biotools:silva", "version": [], "otherID": [ { "value": "RRID:SCR_006423", "type": "rrid", "version": null } ], "relation": [ { "biotoolsID": "silvangs", "type": "usedBy" }, { "biotoolsID": "d3hub", "type": "includedIn" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0224", "term": "Query and retrieval" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1097", "term": "Sequence accession (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_1964", "term": "plain text format (unformatted)" } ] }, { "data": { "uri": "http://edamontology.org/data_1868", "term": "Taxon" }, "format": [ { "uri": "http://edamontology.org/format_1964", "term": "plain text format (unformatted)" } ] }, { "data": { "uri": "http://edamontology.org/data_1046", "term": "Strain name" }, "format": [ { "uri": "http://edamontology.org/format_1964", "term": "plain text format (unformatted)" } ] }, { "data": { "uri": "http://edamontology.org/data_1088", "term": "Article ID" }, "format": [ { "uri": "http://edamontology.org/format_1964", "term": "plain text format (unformatted)" } ] }, { "data": { "uri": "http://edamontology.org/data_2909", "term": "Organism name" }, "format": [ { "uri": "http://edamontology.org/format_1964", "term": "plain text format (unformatted)" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2955", "term": "Sequence report" }, "format": [ { "uri": "http://edamontology.org/format_2331", "term": "HTML" } ] }, { "data": { "uri": "http://edamontology.org/data_1383", "term": "Sequence alignment (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_3830", "term": "ARB" }, { "uri": "http://edamontology.org/format_1984", "term": "FASTA-aln" } ] }, { "data": { "uri": "http://edamontology.org/data_2977", "term": "Nucleic acid sequence" }, "format": [ { "uri": "http://edamontology.org/format_3830", "term": "ARB" }, { "uri": "http://edamontology.org/format_1984", "term": "FASTA-aln" } ] } ], "note": "The search and retrieval functions of the SILVA website can be used to build custom subsets of sequences. In addition to simple searches e.g. for accession numbers, organism names, taxonomic entities, or publication DOI/PubMed IDs, complex queries over several database fields using constraints such as sequence length or quality values are possible. The results can be sorted according to accession numbers, organism names, sequence length, sequence and alignment quality and Pintail values. The search results show accession number, organism name, sequence length, sequence quality values, taxonomic classifications, and links to view the full sequence record on SILVA and on ENA. Sequences found via search and added to download cart can be downloaded as FASTA and ARB files.", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_2419", "term": "Primer and probe design" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2977", "term": "Nucleic acid sequence" }, "format": [ { "uri": "http://edamontology.org/format_1207", "term": "nucleotide" } ] }, { "data": { "uri": "http://edamontology.org/data_1240", "term": "PCR primers" }, "format": [ { "uri": "http://edamontology.org/format_1207", "term": "nucleotide" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2048", "term": "Report" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" }, { "uri": "http://edamontology.org/format_2331", "term": "HTML" } ] }, { "data": { "uri": "http://edamontology.org/data_0850", "term": "Sequence set" }, "format": [ { "uri": "http://edamontology.org/format_2333", "term": "Binary format" } ] }, { "data": { "uri": "http://edamontology.org/data_1383", "term": "Nucleic acid sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_3830", "term": "ARB" }, { "uri": "http://edamontology.org/format_1984", "term": "FASTA-aln" } ] }, { "data": { "uri": "http://edamontology.org/data_2977", "term": "Nucleic acid sequence" }, "format": [ { "uri": "http://edamontology.org/format_3830", "term": "ARB" }, { "uri": "http://edamontology.org/format_1984", "term": "FASTA-aln" } ] } ], "note": "The SILVA Probe Match and Evaluation Tool detects and displays all occurrences of a given probe or primer sequence in the SILVA datasets. \n\nTestPrime allows you to evaluate the performance of primer pairs by running an in silico PCR on the SILVA databases. From the results of the PCR, TestPrime computes coverages for each taxonomic group in all of the taxonomies offered by SILVA.", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0492", "term": "Multiple sequence alignment" }, { "uri": "http://edamontology.org/operation_0496", "term": "Global alignment" }, { "uri": "http://edamontology.org/operation_3460", "term": "Taxonomic classification" }, { "uri": "http://edamontology.org/operation_0547", "term": "Phylogenetic inference (maximum likelihood and Bayesian methods)" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2977", "term": "Nucleic acid sequence" }, "format": [ { "uri": "http://edamontology.org/format_1984", "term": "FASTA-aln" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1383", "term": "Nucleic acid sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_3830", "term": "ARB" }, { "uri": "http://edamontology.org/format_1984", "term": "FASTA-aln" } ] }, { "data": { "uri": "http://edamontology.org/data_0867", "term": "Sequence alignment report" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" }, { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] }, { "data": { "uri": "http://edamontology.org/data_0872", "term": "Phylogenetic tree" }, "format": [ { "uri": "http://edamontology.org/format_1910", "term": "newick" } ] }, { "data": { "uri": "http://edamontology.org/data_1872", "term": "Taxonomic classification" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" } ] } ], "note": "The Alignment, Classification and Tree Service (ACT) of SILVA allows to align and optionally classify sequences using the SILVA Incremental Aligner (SINA). From aligned sequences, (optionally) phylogenetic trees can be inferred using FastTree or RAxML.", "cmd": null } ], "toolType": [ "Web application", "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_0659", "term": "Functional, regulatory and non-coding RNA" }, { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/topic_3293", "term": "Phylogenetics" }, { "uri": "http://edamontology.org/topic_0637", "term": "Taxonomy" }, { "uri": "http://edamontology.org/topic_3050", "term": "Biodiversity" }, { "uri": "http://edamontology.org/topic_3301", "term": "Microbiology" }, { "uri": "http://edamontology.org/topic_0632", "term": "Probes and primers" } ], "operatingSystem": [], "language": [], "license": "CC-BY-4.0", "collectionID": [ "de.NBI", "de.NBI-biodata", "DSMZ Digital Diversity" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [ "Data" ], "elixirNode": [ "Germany" ], "elixirCommunity": [], "link": [ { "url": "https://www.arb-silva.de/browser/", "type": [ "Service" ], "note": "SILVA Taxonomy Browser" }, { "url": "https://www.arb-silva.de/search/", "type": [ "Service" ], "note": "SILVA metadata search" }, { "url": "https://www.arb-silva.de/aligner/", "type": [ "Service" ], "note": "ACT: Alignment, Classification and Tree Service" }, { "url": "https://www.arb-silva.de/search/testprobe/", "type": [ "Service" ], "note": "SILVA Probe Match and Evaluation Tool" }, { "url": "https://www.arb-silva.de/search/testprime/", "type": [ "Service" ], "note": "SILVA Primer Evaluation Tool" }, { "url": "https://treeviewer.arb-silva.de/", "type": [ "Service" ], "note": "Web-based viewer for the SILVA guide trees" } ], "download": [ { "url": "https://www.arb-silva.de/download/archive/", "type": "Downloads page", "note": "SILVA dataset archive", "version": null } ], "documentation": [ { "url": "https://www.arb-silva.de/silva-license-information/", "type": [ "Terms of use" ], "note": null }, { "url": "https://www.arb-silva.de/contact/", "type": [ "Citation instructions" ], "note": null }, { "url": "https://www.arb-silva.de/documentation/", "type": [ "General" ], "note": null }, { "url": "https://www.arb-silva.de/documentation/faqs/", "type": [ "FAQ" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gks1219", "pmid": "23193283", "pmcid": "PMC3531112", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "The SILVA ribosomal RNA gene database project: Improved data processing and web-based tools", "abstract": "SILVA (from Latin silva, forest, http://www.arb-silva.de) is a comprehensive web resource for up to date, quality-controlled databases of aligned ribosomal RNA (rRNA) gene sequences from the Bacteria, Archaea and Eukaryota domains and supplementary online services. The referred database release 111 (July 2012) contains 3194 778 small subunit and 288717 large subunit rRNA gene sequences. Since the initial description of the project, substantial new features have been introduced, including advanced quality control procedures, an improved rRNA gene aligner, online tools for probe and primer evaluation and optimized browsing, searching and downloading on the website. Furthermore, the extensively curated SILVA taxonomy and the new non-redundant SILVA datasets provide an ideal reference for high-throughput classification of data from next-generation sequencing approaches. © The Author(s) 2012.", "date": "2013-01-01T00:00:00Z", "citationCount": 22633, "authors": [ { "name": "Quast C." }, { "name": "Pruesse E." }, { "name": "Yilmaz P." }, { "name": "Gerken J." }, { "name": "Schweer T." }, { "name": "Yarza P." }, { "name": "Peplies J." }, { "name": "Glockner F.O." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/nar/gkt1209", "pmid": "24293649", "pmcid": "PMC3965112", "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "The SILVA and \"all-species Living Tree Project (LTP)\" taxonomic frameworks", "abstract": "SILVA (from Latin silva, forest, http://www.arb-silva.de) is a comprehensive resource for up-to-date quality-controlled databases of aligned ribosomal RNA (rRNA) gene sequences from the Bacteria, Archaea and Eukaryota domains and supplementary online services. SILVA provides a manually curated taxonomy for all three domains of life, based on representative phylogenetic trees for the small- and large-subunit rRNA genes. This article describes the improvements the SILVA taxonomy has undergone in the last 3 years. Specifically we are focusing on the curation process, the various resources used for curation and the comparison of the SILVA taxonomy with Greengenes and RDP-II taxonomies. Our comparisons not only revealed a reasonable overlap between the taxa names, but also points to significant differences in both names and numbers of taxa between the three resources. © 2013 The Author(s). Published by Oxford University Press.", "date": "2014-01-01T00:00:00Z", "citationCount": 2590, "authors": [ { "name": "Yilmaz P." }, { "name": "Parfrey L.W." }, { "name": "Yarza P." }, { "name": "Gerken J." }, { "name": "Pruesse E." }, { "name": "Quast C." }, { "name": "Schweer T." }, { "name": "Peplies J." }, { "name": "Ludwig W." }, { "name": "Glockner F.O." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/nar/gkm864", "pmid": "17947321", "pmcid": "PMC2175337", "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "SILVA: A comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB", "abstract": "Sequencing ribosomal RNA (rRNA) genes is currently the method of choice for phylogenetic reconstruction, nucleic acid based detection and quantification of microbial diversity. The ARB software suite with its corresponding rRNA datasets has been accepted by researchers worldwide as a standard tool for large scale rRNA analysis. However, the rapid increase of publicly available rRNA sequence data has recently hampered the maintenance of comprehensive and curated rRNA knowledge databases. A new system, SILVA (from Latin silva, forest), was implemented to provide a central comprehensive web resource for up to date, quality controlled databases of aligned rRNA sequences from the Bacteria, Archaea and Eukarya domains. All sequences are checked for anomalies, carry a rich set of sequence associated contextual information, have multiple taxonomic classifications, and the latest validly described nomenclature. Furthermore, two precompiled sequence datasets compatible with ARB are offered for download on the SILVA website: (i) the reference (Ref) datasets, comprising only high quality, nearly full length sequences suitable for in-depth phylogenetic analysis and probe design and (ii) the comprehensive Parc datasets with all publicly available rRNA sequences longer than 300 nucleotides suitable for biodiversity analyses. The latest publicly available database release 91 (August 2007) hosts 547 521 sequences split into 461 823 small subunit and 85 689 large subunit rRNAs. © 2007 The Author(s).", "date": "2007-12-01T00:00:00Z", "citationCount": 5291, "authors": [ { "name": "Pruesse E." }, { "name": "Quast C." }, { "name": "Knittel K." }, { "name": "Fuchs B.M." }, { "name": "Ludwig W." }, { "name": "Peplies J." }, { "name": "Glockner F.O." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/bioinformatics/bts252", "pmid": "22556368", "pmcid": "PMC3389763", "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes", "abstract": "Motivation: In the analysis of homologous sequences, computation of multiple sequence alignments (MSAs) has become a bottleneck. This is especially troublesome for marker genes like the ribosomal RNA (rRNA) where already millions of sequences are publicly available and individual studies can easily produce hundreds of thousands of new sequences. Methods have been developed to cope with such numbers, but further improvements are needed to meet accuracy requirements.Results: In this study, we present the SILVA Incremental Aligner (SINA) used to align the rRNA gene databases provided by the SILVA ribosomal RNA project. SINA uses a combination of k-mer searching and partial order alignment (POA) to maintain very high alignment accuracy while satisfying high throughput performance demands. SINA was evaluated in comparison with the commonly used high throughput MSA programs PyNAST and mothur. The three BRAliBase III benchmark MSAs could be reproduced with 99.3, 97.6 and 96.1 accuracy. A larger benchmark MSA comprising 38 772 sequences could be reproduced with 98.9 and 99.3% accuracy using reference MSAs comprising 1000 and 5000 sequences. SINA was able to achieve higher accuracy than PyNAST and mothur in all performed benchmarks. © The Author(s) 2012. Published by Oxford University Press.", "date": "2012-07-01T00:00:00Z", "citationCount": 2408, "authors": [ { "name": "Pruesse E." }, { "name": "Peplies J." }, { "name": "Glockner F.O." } ], "journal": "Bioinformatics" } }, { "doi": "10.1016/j.jbiotec.2017.06.1198", "pmid": "28648396", "pmcid": null, "type": [ "Review" ], "version": null, "note": null, "metadata": { "title": "25 years of serving the community with ribosomal RNA gene reference databases and tools", "abstract": "SILVA (lat. forest) is a comprehensive web resource, providing services around up to date, high-quality datasets of aligned ribosomal RNA gene (rDNA) sequences from the Bacteria, Archaea, and Eukaryota domains. SILVA dates back to the year 1991 when Dr. Wolfgang Ludwig from the Technical University Munich started the integrated software workbench ARB (lat. tree) to support high-quality phylogenetic inference and taxonomy based on the SSU and LSU rDNA marker genes. At that time, the ARB project maintained both, the sequence reference datasets and the software package for data analysis. In 2005, with the massive increase of DNA sequence data, the maintenance of the software system ARB and the corresponding rRNA databases SILVA was split between Munich and the Microbial Genomics and Bioinformatics Research Group in Bremen. ARB has been continuously developed to include new features and improve the usability of the workbench. Thousands of users worldwide appreciate the seamless integration of common analysis tools under a central graphical user interface, in combination with its versatility. The first SILVA release was deployed in February 2007 based on the EMBL-EBI/ENA release 89. Since then, full SILVA releases offering the database content in various flavours are published at least annually, complemented by intermediate web-releases where only the SILVA web dataset is updated. SILVA is the only rDNA database project worldwide where special emphasis is given to the consistent naming of clades of uncultivated (environmental) sequences, where no validly described cultivated representatives are available. Also exclusive for SILVA is the maintenance of both comprehensive aligned 16S/18S rDNA and 23S/28S rDNA sequence datasets. Furthermore, the SILVA alignments and trees were designed to include Eukaryota, another unique feature among rDNA databases. With the termination of the European Ribosomal RNA Database Project in 2007, the SILVA database has become the authoritative rDNA database project for Europe. The application spectrum of ARB and SILVA ranges from biodiversity analysis, medical diagnostics, to biotechnology and quality control for academia and industry.", "date": "2017-11-10T00:00:00Z", "citationCount": 635, "authors": [ { "name": "Glockner F.O." }, { "name": "Yilmaz P." }, { "name": "Quast C." }, { "name": "Gerken J." }, { "name": "Beccati A." }, { "name": "Ciuprina A." }, { "name": "Bruns G." }, { "name": "Yarza P." }, { "name": "Peplies J." }, { "name": "Westram R." }, { "name": "Ludwig W." } ], "journal": "Journal of Biotechnology" } }, { "doi": "10.1186/s12859-017-1841-3", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "SILVA tree viewer: Interactive web browsing of the SILVA phylogenetic guide trees", "abstract": "Background: Phylogenetic trees are an important tool to study the evolutionary relationships among organisms. The huge amount of available taxa poses difficulties in their interactive visualization. This hampers the interaction with the users to provide feedback for the further improvement of the taxonomic framework. Results: The SILVA Tree Viewer is a web application designed for visualizing large phylogenetic trees without requiring the download of any software tool or data files. The SILVA Tree Viewer is based on Web Geographic Information Systems (Web-GIS) technology with a PostgreSQL backend. It enables zoom and pan functionalities similar to Google Maps. The SILVA Tree Viewer enables access to two phylogenetic (guide) trees provided by the SILVA database: the SSU Ref NR99 inferred from high-quality, full-length small subunit sequences, clustered at 99% sequence identity and the LSU Ref inferred from high-quality, full-length large subunit sequences. Conclusions: The Tree Viewer provides tree navigation, search and browse tools as well as an interactive feedback system to collect any kinds of requests ranging from taxonomy to data curation and improving the tool itself.", "date": "2017-09-30T00:00:00Z", "citationCount": 29, "authors": [ { "name": "Beccati A." }, { "name": "Gerken J." }, { "name": "Quast C." }, { "name": "Yilmaz P." }, { "name": "Glockner F.O." } ], "journal": "BMC Bioinformatics" } } ], "credit": [ { "name": "Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures", "email": "hub@dsmz.de", "url": "https://www.dsmz.de", "orcidid": null, "gridid": "grid.420081.f", "rorid": "02tyer376", "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "SILVA Team", "email": "contact@arb-silva.de", "url": "https://www.arb-silva.de/contact/team/", "orcidid": null, "gridid": "grid.507782.f", "rorid": "027z9pz32", "fundrefid": null, "typeEntity": "Division", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "silva", "additionDate": "2016-09-30T15:59:05Z", "lastUpdate": "2025-06-30T13:26:42.882897Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "Zoonomia", "description": "The Zoonomia Project provides access to genomic data including assemblies, annotations and alignments for 240 mammalian species.", "homepage": "https://zoonomiaproject.org/", "biotoolsID": "zoonomiaproject", "biotoolsCURIE": "biotools:zoonomiaproject", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2422", "term": "Data retrieval" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2909", "term": "Organism name" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1045", "term": "Species name" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1383", "term": "Nucleic acid sequence alignment" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_3002", "term": "Annotation track" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_0925", "term": "Sequence assembly" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_3050", "term": "Biodiversity" } ], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "owner": "adriaan", "additionDate": "2025-06-16T13:44:36.983992Z", "lastUpdate": "2025-06-16T13:51:19.876113Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "MuGVRE", "description": "The MuG Virtual Research Environment is an analysis platform for 3D/4D genomics analyses. It integrates genomics tools for chromatin dynamics data.", "homepage": "https://www.multiscalegenomics.eu/", "biotoolsID": "mugvre", "biotoolsCURIE": "biotools:mugvre", "version": [ "1.0" ], "otherID": [], "relation": [ { "biotoolsID": "nucleosome_dynamics", "type": "includes" }, { "biotoolsID": "tadbit", "type": "includes" }, { "biotoolsID": "jbrowse", "type": "includes" }, { "biotoolsID": "ngl", "type": "includes" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0292", "term": "Sequence alignment" }, { "uri": "http://edamontology.org/operation_3198", "term": "Read mapping" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2044", "term": "Sequence" }, "format": [ { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" }, { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_3210", "term": "Genome index" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_2572", "term": "BAM" } ] } ], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0475", "term": "Nucleic acid structure prediction" }, { "uri": "http://edamontology.org/operation_2426", "term": "Modelling and simulation" }, { "uri": "http://edamontology.org/operation_0279", "term": "Nucleic acid folding analysis" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2977", "term": "Nucleic acid sequence" }, "format": [ { "uri": "http://edamontology.org/format_2200", "term": "FASTA-like (text)" } ] }, { "data": { "uri": "http://edamontology.org/data_1255", "term": "Sequence features" }, "format": [ { "uri": "http://edamontology.org/format_2305", "term": "GFF" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3870", "term": "Trajectory data" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1460", "term": "Protein structure" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] } ], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0478", "term": "Molecular docking" }, { "uri": "http://edamontology.org/operation_3900", "term": "DNA-binding protein prediction" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1460", "term": "Protein structure" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2877", "term": "Protein complex" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] } ], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3222", "term": "Peak calling" }, { "uri": "http://edamontology.org/operation_1781", "term": "Gene regulatory network analysis" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0905", "term": "Protein interaction raw data" }, "format": [ { "uri": "http://edamontology.org/format_2572", "term": "BAM" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1276", "term": "Nucleic acid features" }, "format": [ { "uri": "http://edamontology.org/format_3003", "term": "BED" } ] } ], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3927", "term": "Network analysis" }, { "uri": "http://edamontology.org/operation_0279", "term": "Nucleic acid folding analysis" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0905", "term": "Protein interaction raw data" }, "format": [ { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3872", "term": "Topology data" }, "format": [ { "uri": "http://edamontology.org/format_4002", "term": "pickle" } ] }, { "data": { "uri": "http://edamontology.org/data_0906", "term": "Protein interaction data" }, "format": [ { "uri": "http://edamontology.org/format_4002", "term": "pickle" } ] } ], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_2478", "term": "Nucleic acid sequence analysis" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1461", "term": "Protein-ligand complex" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2084", "term": "Nucleic acid report" }, "format": [] } ], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_2476", "term": "Molecular dynamics" }, { "uri": "http://edamontology.org/operation_2481", "term": "Nucleic acid structure analysis" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0883", "term": "Structure" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3870", "term": "Trajectory data" }, "format": [] } ], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0432", "term": "Nucleosome position prediction" }, { "uri": "http://edamontology.org/operation_3454", "term": "Phasing" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0905", "term": "Protein interaction raw data" }, "format": [ { "uri": "http://edamontology.org/format_2572", "term": "BAM" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3002", "term": "Annotation track" }, "format": [ { "uri": "http://edamontology.org/format_2305", "term": "GFF" } ] } ], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0337", "term": "Visualisation" }, { "uri": "http://edamontology.org/operation_0570", "term": "Structure visualisation" }, { "uri": "http://edamontology.org/operation_0564", "term": "Sequence visualisation" }, { "uri": "http://edamontology.org/operation_3925", "term": "Network visualisation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2012", "term": "Sequence coordinates" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_3002", "term": "Annotation track" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_3869", "term": "Simulation" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_0883", "term": "Structure" }, "format": [] } ], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application", "Workbench" ], "topic": [ { "uri": "http://edamontology.org/topic_3176", "term": "DNA packaging" }, { "uri": "http://edamontology.org/topic_3169", "term": "ChIP-seq" }, { "uri": "http://edamontology.org/topic_0097", "term": "Nucleic acid structure analysis" }, { "uri": "http://edamontology.org/topic_2275", "term": "Molecular modelling" } ], "operatingSystem": [], "language": [ "PHP", "Python" ], "license": "Apache-2.0", "collectionID": [ "RIS3CAT VEIS" ], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "http://vre.multiscalegenomics.eu", "type": [ "Service" ], "note": null }, { "url": "https://github.com/Multiscale-Genomics/VRE", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [ { "url": "https://www.multiscalegenomics.eu/MuGVRE/terms-of-use/", "type": [ "Terms of use" ], "note": null }, { "url": "http://vre.multiscalegenomics.eu/help/starting.php", "type": [ "Quick start guide" ], "note": null }, { "url": "https://www.multiscalegenomics.eu/MuGVRE/training/", "type": [ "Training material" ], "note": null } ], "publication": [ { "doi": "10.1101/602474", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": "1.0", "note": null, "metadata": null } ], "credit": [ { "name": "Laia Codó", "email": "laia.codo@bsc.es", "url": null, "orcidid": "https://orcid.org/0000-0002-6797-8746", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Josep Lluís Gelpí", "email": null, "url": null, "orcidid": "http://orcid.org/0000-0002-0566-7723", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Multiscale Complex Genomics Community", "email": "vre@multiscalegenomics.eu", "url": "https://www.multiscalegenomics.eu/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Consortium", "typeRole": [ "Developer" ], "note": null } ], "owner": "lcodo", "additionDate": "2021-01-12T12:02:47Z", "lastUpdate": "2025-05-29T11:46:19.236621Z", "editPermission": { "type": "group", "authors": [ "gelpi@ub.edu" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "BioSurfDB", "description": "BioSurfDB is a online database for biodegradation and biosurfactants.", "homepage": "https://www.biosurfdb.org", "biotoolsID": "biosurfdb", "biotoolsCURIE": "biotools:biosurfdb", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0495", "term": "Local alignment" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3494", "term": "DNA sequence" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2886", "term": "Protein sequence record" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1383", "term": "Nucleic acid sequence alignment" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1385", "term": "Hybrid sequence alignment" }, "format": [] } ], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0349", "term": "Sequence database search (by property)" } ], "input": [], "output": [ { "data": { "uri": "http://edamontology.org/data_1026", "term": "Gene symbol" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1027", "term": "Gene ID (NCBI)" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2299", "term": "Gene name" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_3494", "term": "DNA sequence" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_3297", "term": "Biotechnology" }, { "uri": "http://edamontology.org/topic_3301", "term": "Microbiology" }, { "uri": "http://edamontology.org/topic_0821", "term": "Enzymes" } ], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.1093/database/bav033", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "BioSurfDB: Knowledge and algorithms to support biosurfactants and biodegradation studies", "abstract": "Crude oil extraction, transportation and use provoke the contamination of countless ecosystems. Therefore, bioremediation through surfactants mobilization or biodegradation is an important subject, both economically and environmentally. Bioremediation research had a great boost with the recent advances in Metagenomics, as it enabled the sequencing of uncultured microorganisms providing new insights on surfactant-producing and/or oil-degrading bacteria. Many research studies are making available genomic data from unknown organisms obtained from metagenomics analysis of oil-contaminated environmental samples. These new datasets are presently demanding the development of new tools and data repositories tailored for the biological analysis in a context of bioremediation data analysis. This work presents BioSurfDB, www.biosurfdb.org, a curated relational information system integrating data from: (i) metagenomes; (ii) organisms; (iii) biodegradation relevant genes; proteins and their metabolic pathways; (iv) bioremediation experiments results, with specific pollutants treatment efficiencies by surfactant producing organisms; and (v) a biosurfactant-curated list, grouped by producing organism, surfactant name, class and reference. The main goal of this repository is to gather information on the characterization of biological compounds and mechanisms involved in biosurfactant production and/or biodegradation and make it available in a curated way and associated with a number of computational tools to support studies of genomic and metagenomic data.", "date": "2015-01-01T00:00:00Z", "citationCount": 30, "authors": [ { "name": "Oliveira J.S." }, { "name": "Araujo W." }, { "name": "Sales A.I.L." }, { "name": "De Brito Guerra A." }, { "name": "Da Silva Araujo S.C." }, { "name": "De Vasconcelos A.T.R." }, { "name": "Agnez-Lima L.F." }, { "name": "Freitas A.T." } ], "journal": "Database" } } ], "credit": [ { "name": "Jorge S. Oliveira", "email": "jorge.oliveira@tecnico.ulisboa.pt", "url": "https://web.tecnico.ulisboa.pt/jorge.oliveira/", "orcidid": "https://orcid.org/0000-0001-6425-2176", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Ana Teresa Freitas", "email": "ana.freitas@tecnico.ulisboa.pt", "url": null, "orcidid": "http://orcid.org/0000-0003-4638-2879", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Ana Tereza Ribeiro de Vasconcelos", "email": "atrv@lncc.br", "url": null, "orcidid": "http://orcid.org/0000-0002-4632-2086", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Lucymara Fassarella Agnez-Lima", "email": "lucymara.agnez@ufrn.br", "url": null, "orcidid": "http://orcid.org/0000-0003-0642-3162", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Gil Poiares-Oliveira", "email": "gpo@biodata.pt", "url": "https://web.tecnico.ulisboa.pt/gil.oliveira", "orcidid": "https://orcid.org/0000-0003-4638-2879", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Maintainer" ], "note": null } ], "owner": "ELIXIR-PT", "additionDate": "2025-04-29T17:07:56.642694Z", "lastUpdate": "2025-04-29T17:35:41.655075Z", "editPermission": { "type": "group", "authors": [ "gpo" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "samclip", "description": "Filter SAM file for soft and hard clipped alignments", "homepage": "https://github.com/tseemann/samclip", "biotoolsID": "samclip", "biotoolsCURIE": "biotools:samclip", "version": [ "0.4.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3192", "term": "Sequence trimming" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1383", "term": "Nucleic acid sequence alignment" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1383", "term": "Nucleic acid sequence alignment" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" }, { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" }, { "uri": "http://edamontology.org/topic_0102", "term": "Mapping" } ], "operatingSystem": [ "Linux", "Mac" ], "language": [ "Perl" ], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/tseemann/samclip", "type": [ "Repository" ], "note": null } ], "download": [ { "url": "https://anaconda.org/bioconda/samclip", "type": "Software package", "note": null, "version": "0.4.0" } ], "documentation": [ { "url": "https://github.com/tseemann/samclip", "type": [ "General" ], "note": null } ], "publication": [], "credit": [], "owner": "emmcauley", "additionDate": "2025-04-21T21:06:51.624399Z", "lastUpdate": "2025-04-21T21:06:51.626575Z", "editPermission": { "type": "group", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "TREND Protein Evolution Function", "description": "TREND is a platform that allows researchers to explore protein function and evolution identifying protein features, gene neighborhoods and operons, clustering neighboring genes, and integrating all these data into phylogenomic context and cross-referencing with RefSeq, Pfam, CDD and MiST databases. The platform provides ample opportunities for adjusting each step of the analysis.", "homepage": "http://trend.evobionet.com/", "biotoolsID": "trend_protein_evolution_function", "biotoolsCURIE": "biotools:trend_protein_evolution_function", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0492", "term": "Multiple sequence alignment" }, { "uri": "http://edamontology.org/operation_0323", "term": "Phylogenetic inference" }, { "uri": "http://edamontology.org/operation_0291", "term": "Sequence clustering" }, { "uri": "http://edamontology.org/operation_2995", "term": "Sequence classification" }, { "uri": "http://edamontology.org/operation_0246", "term": "Protein domain recognition" }, { "uri": "http://edamontology.org/operation_3092", "term": "Protein feature detection" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1384", "term": "Protein sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_1233", "term": "Sequence set (protein)" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_0872", "term": "Phylogenetic tree" }, "format": [ { "uri": "http://edamontology.org/format_1910", "term": "newick" } ] }, { "data": { "uri": "http://edamontology.org/data_1900", "term": "NCBI locus tag" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] }, { "data": { "uri": "http://edamontology.org/data_2385", "term": "RefSeq accession (protein)" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1384", "term": "Protein sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_0872", "term": "Phylogenetic tree" }, "format": [ { "uri": "http://edamontology.org/format_1910", "term": "newick" } ] }, { "data": { "uri": "http://edamontology.org/data_1277", "term": "Protein features" }, "format": [ { "uri": "http://edamontology.org/format_3464", "term": "JSON" } ] }, { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3604", "term": "SVG" } ] }, { "data": { "uri": "http://edamontology.org/data_1245", "term": "Sequence cluster (protein)" }, "format": [ { "uri": "http://edamontology.org/format_3464", "term": "JSON" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Web service" ], "topic": [ { "uri": "http://edamontology.org/topic_3299", "term": "Evolutionary biology" }, { "uri": "http://edamontology.org/topic_0084", "term": "Phylogeny" }, { "uri": "http://edamontology.org/topic_3301", "term": "Microbiology" }, { "uri": "http://edamontology.org/topic_3510", "term": "Protein sites, features and motifs" }, { "uri": "http://edamontology.org/topic_0085", "term": "Functional genomics" }, { "uri": "http://edamontology.org/topic_0194", "term": "Phylogenomics" }, { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" } ], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "http://trend.evobionet.com/help", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gkaa243", "pmid": "32282909", "pmcid": "PMC7319448", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "TREND: a platform for exploring protein function in prokaryotes based on phylogenetic, domain architecture and gene neighborhood analyses", "abstract": "Key steps in a computational study of protein function involve analysis of (i) relationships between homologous proteins, (ii) protein domain architecture and (iii) gene neighborhoods the corresponding proteins are encoded in. Each of these steps requires a separate computational task and sets of tools. Currently in order to relate protein features and gene neighborhoods information to phylogeny, researchers need to prepare all the necessary data and combine them by hand, which is time-consuming and error-prone. Here, we present a new platform, TREND (tree-based exploration of neighborhoods and domains), which can perform all the necessary steps in automated fashion and put the derived information into phylogenomic context, thus making evolutionary based protein function analysis more efficient. A rich set of adjustable components allows a user to run the computational steps specific to his task. TREND is freely available at http://trend.zhulinlab.org.", "date": "2021-01-01T00:00:00Z", "citationCount": 33, "authors": [ { "name": "Gumerov V.M." }, { "name": "Zhulin I.B." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/nar/gkac034", "pmid": "35100406", "pmcid": "PMC8860576", "type": [ "Other" ], "version": null, "note": "Can be also accessed at this URL: https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkac034/6517937", "metadata": { "title": "Erratum: TREND: A platform for exploring protein function in prokaryotes based on phylogenetic, domain architecture and gene neighborhood analyses (Nucleic Acids Research DOI: 10.1093/nar/gkaa243)", "abstract": "TheURL address of the web server published in this article has been changed fromhttp://trend.zhulinlab.org to http://trend. evobionet.com/.", "date": "2022-02-22T00:00:00Z", "citationCount": 6, "authors": [ { "name": "Gumerov V.M." }, { "name": "Zhulin I.B." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "Vadim Gumerov", "email": "gumerov.1@osu.edu", "url": null, "orcidid": "https://orcid.org/0000-0003-1670-7679", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "vadim", "additionDate": "2020-11-09T21:38:53Z", "lastUpdate": "2024-12-17T20:42:49.942166Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "msa", "description": "Display multiple-sequence alignment. The tool is also available as R/BioConductor interface to the multiple sequence alignment algorithms ClustalW, ClustalOmega, and Muscle. All three algorithms are integrated in the package, therefore, they do not depend on any external software tools and are available for all major platforms.", "homepage": "http://msa.biojs.net", "biotoolsID": "msa", "biotoolsCURIE": "biotools:msa", "version": [ "1.0.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0564", "term": "Sequence visualisation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_1982", "term": "ClustalW format" }, { "uri": "http://edamontology.org/format_1984", "term": "FASTA-aln" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_1984", "term": "FASTA-aln" } ] }, { "data": { "uri": "http://edamontology.org/data_1711", "term": "Sequence alignment image" }, "format": [ { "uri": "http://edamontology.org/format_3547", "term": "Image format" } ] }, { "data": { "uri": "http://edamontology.org/data_0850", "term": "Sequence set" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_1270", "term": "Feature table" }, "format": [ { "uri": "http://edamontology.org/format_2305", "term": "GFF" } ] } ], "note": "Visualizes multiple sequence alignment, calculates conservation, shows sequence logo, applies multiple color schemes A multiple sequence alignment (ClustalW, FASTA, ...) Exports selected sequences and regions from the alignment Images are exported in PNG Export sequences in FASTA format Export features in GFF\nNOTE: Actually, all these output types of data should instead be under separate \"constant\" operations, while the visualisation should be an unary operation, perhaps without an output.", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0492", "term": "Multiple sequence alignment" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2977", "term": "Nucleic acid sequence" }, "format": [ { "uri": "http://edamontology.org/format_1948", "term": "nbrf/pir" }, { "uri": "http://edamontology.org/format_1929", "term": "FASTA" }, { "uri": "http://edamontology.org/format_1935", "term": "GCG" }, { "uri": "http://edamontology.org/format_1997", "term": "PHYLIP format" }, { "uri": "http://edamontology.org/format_1927", "term": "EMBL format" }, { "uri": "http://edamontology.org/format_1936", "term": "GenBank format" } ] }, { "data": { "uri": "http://edamontology.org/data_2976", "term": "Protein sequence" }, "format": [ { "uri": "http://edamontology.org/format_1948", "term": "nbrf/pir" }, { "uri": "http://edamontology.org/format_1929", "term": "FASTA" }, { "uri": "http://edamontology.org/format_1935", "term": "GCG" }, { "uri": "http://edamontology.org/format_1997", "term": "PHYLIP format" }, { "uri": "http://edamontology.org/format_1927", "term": "EMBL format" }, { "uri": "http://edamontology.org/format_1936", "term": "GenBank format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0867", "term": "Sequence alignment report" }, "format": [ { "uri": "http://edamontology.org/format_1982", "term": "ClustalW format" }, { "uri": "http://edamontology.org/format_1929", "term": "FASTA" }, { "uri": "http://edamontology.org/format_1997", "term": "PHYLIP format" }, { "uri": "http://edamontology.org/format_3508", "term": "PDF" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool", "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/topic_0160", "term": "Sequence sites, features and motifs" }, { "uri": "http://edamontology.org/topic_3293", "term": "Phylogenetics" }, { "uri": "http://edamontology.org/topic_3168", "term": "Sequencing" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "JavaScript" ], "license": "Apache-2.0", "collectionID": [ "Rostlab tools", "Bioconductor", "BioJS" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/wilzbach/msa", "type": [ "Repository" ], "note": null }, { "url": "http://biojs.io/", "type": [ "Software catalogue" ], "note": null }, { "url": "http://github.com/wilzbach/msa", "type": [ "Helpdesk" ], "note": null }, { "url": "http://www.bioinf.jku.at/software/msa/", "type": [ "Mirror" ], "note": null } ], "download": [ { "url": "https://github.com/wilzbach/msa", "type": "Source code", "note": null, "version": null }, { "url": "https://cdn.bio.sh/", "type": "Binaries", "note": null, "version": null } ], "documentation": [ { "url": "https://github.com/wilzbach/msa/blob/master/LICENSE", "type": [ "Terms of use" ], "note": null }, { "url": "http://msa.biojs.net", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btw474", "pmid": "27412096", "pmcid": "PMC5181560", "type": [ "Primary" ], "version": null, "note": null, "metadata": null }, { "doi": "10.1093/bioinformatics/btv494", "pmid": "26315911", "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Sebastian Wilzbach", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Ian Sillitoe", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Contributor" ], "note": null }, { "name": "Guy Yachdav", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Contributor" ], "note": null }, { "name": "Benedikt Rauscher", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Contributor" ], "note": null }, { "name": "Tatyana Goldberg", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Contributor" ], "note": null }, { "name": "Technische Universität München", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Google Summer of Code (GSoC) 2014", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [ "Contributor" ], "note": null }, { "name": "BioJS", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": null, "email": null, "url": "http://github.com/wilzbach/msa", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Ulrich Bodenhofer", "email": "bodenhofer@bioinf.jku.at", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "BioJS", "additionDate": "2016-06-02T02:47:10Z", "lastUpdate": "2024-11-25T16:17:03.898741Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Crispi", "description": "A CRISPR Interactive database.", "homepage": "http://crispi.genouest.org/", "biotoolsID": "crispi", "biotoolsCURIE": "biotools:crispi", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0338", "term": "Sequence database search" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2044", "term": "Sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "note": "A CRISPR Interactive database", "cmd": null } ], "toolType": [ "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_0160", "term": "Sequence sites, features and motifs" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "http://genoweb1.irisa.fr/Serveur-GPO/outils/repeatsAnalysis/CRISPR/help/crispri.pdf", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btp586", "pmid": "19846435", "pmcid": "PMC2788928", "type": [ "Primary" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "GenOuest", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "GenOuest platform", "email": "support@genouest.org", "url": "http://www.genouest.org", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "GenOuest", "additionDate": "2015-01-21T15:12:23Z", "lastUpdate": "2024-11-25T16:06:25.068541Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Plast", "description": "Parallel Local Alignment Search Tool for Database Comparison.", "homepage": "http://www.irisa.fr/symbiose/projects/plast/", "biotoolsID": "plast", "biotoolsCURIE": "biotools:plast", "version": [ "1.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0495", "term": "Local alignment" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2044", "term": "Sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_2044", "term": "Sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "note": "Sequence alignment", "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": "CECILL-2.0", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://plast.inria.fr/", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1186/1471-2105-10-329", "pmid": "19821978", "pmcid": "PMC2770072", "type": [ "Primary" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "GenOuest", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Dominique Lavenier", "email": "lavenier@irisa.fr", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "GenOuest", "additionDate": "2015-01-21T15:12:23Z", "lastUpdate": "2024-11-25T16:06:23.702130Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "CyanoLyase", "description": "Manually curated sequence and amino acid motif database gathering all the different phycobilin lyases and related protein sequences available in public databases.", "homepage": "http://cyanolyase.genouest.org/", "biotoolsID": "cyanolyase", "biotoolsCURIE": "biotools:cyanolyase", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0253", "term": "Sequence feature detection" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2044", "term": "Sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0858", "term": "Sequence signature matches" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "note": "Motif occurence detection in protein sequences", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0338", "term": "Sequence database search" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2044", "term": "Sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_1333", "term": "BLAST results" } ] } ], "note": "Protein sequence alignment against known family members", "cmd": null } ], "toolType": [ "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_0623", "term": "Gene and protein families" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "http://cyanolyase.genouest.org/help", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gks1091", "pmid": "23175607", "pmcid": "PMC3531064", "type": [ "Primary" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "GenOuest", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "GenOuest", "email": "support@genouest.org", "url": "http://www.genouest.org", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "GenOuest", "additionDate": "2015-01-21T15:12:20Z", "lastUpdate": "2024-11-25T16:06:21.263559Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Slider", "description": "A suite of java classes which provides alignment of Illumina Sequence analyser reads. For alignment it uses base probabilities instead of sequences. It also enambles SNP prediction.", "homepage": "http://www.bcgsc.ca/platform/bioinfo/software/slider", "biotoolsID": "slider", "biotoolsCURIE": "biotools:slider", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3227", "term": "Variant calling" }, { "uri": "http://edamontology.org/operation_0484", "term": "SNP detection" }, { "uri": "http://edamontology.org/operation_0292", "term": "Sequence alignment" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2959", "term": "Nucleic acid probability profile" }, "format": [ { "uri": "http://edamontology.org/format_3033", "term": "Matrix format" } ] }, { "data": { "uri": "http://edamontology.org/data_2093", "term": "Data reference" }, "format": [ { "uri": "http://edamontology.org/format_3033", "term": "Matrix format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1383", "term": "Sequence alignment (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_1921", "term": "Alignment format" } ] }, { "data": { "uri": "http://edamontology.org/data_0867", "term": "Sequence alignment report" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Suite" ], "topic": [ { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/topic_2885", "term": "DNA polymorphism" }, { "uri": "http://edamontology.org/topic_2533", "term": "DNA mutation" }, { "uri": "http://edamontology.org/topic_2269", "term": "Statistics and probability" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Java" ], "license": "AFL-3.0", "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.1093/bioinformatics/btn565", "pmid": "18974170", "pmcid": "PMC2638935", "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Slider support", "email": "nmalhis@bcgsc.ca", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "seqwiki_import", "additionDate": "2017-01-13T13:16:31Z", "lastUpdate": "2024-11-25T16:03:22.897522Z", "editPermission": { "type": "group", "authors": [ "ELIXIR-EE" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "webPRANK", "description": "Multiple sequence alignment tool.", "homepage": "http://www.ebi.ac.uk/goldman-srv/webprank/", "biotoolsID": "webprank", "biotoolsCURIE": "biotools:webprank", "version": [ "1" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0492", "term": "Multiple sequence alignment" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2044", "term": "Sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [ "Goldman Tools", "EBI Tools" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "http://www.ebi.ac.uk/about/terms-of-use", "type": [ "Terms of use" ], "note": null }, { "url": "http://www.ebi.ac.uk/goldman-srv/webprank/", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1186/1471-2105-11-579", "pmid": "21110866", "pmcid": "PMC3009689", "type": [ "Primary" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Goldman group", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Ari Loytynoja", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Nick Goldman", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Contributor" ], "note": null }, { "name": "EMBL-EBI", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": null, "email": "ari@ebi.ac.uk", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Ari Loytynoja", "email": "ari.loytynoja@helsinki.fi", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "EMBL-EBI", "additionDate": "2015-01-29T15:47:27Z", "lastUpdate": "2024-11-25T15:57:33.319602Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "SAS", "description": "Annotation of protein sequence with structural info from similar proteins in the PDB.", "homepage": "http://www.ebi.ac.uk/thornton-srv/databases/sas", "biotoolsID": "sas", "biotoolsCURIE": "biotools:sas", "version": [ "1" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0346", "term": "Sequence similarity search" }, { "uri": "http://edamontology.org/operation_3092", "term": "Protein feature detection" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2976", "term": "Protein sequence" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] }, { "data": { "uri": "http://edamontology.org/data_1277", "term": "Protein features" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] } ], "note": "The ouput is an alignment of the query sequence vs a sequence from PDB, annotated by structural data", "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/topic_0160", "term": "Sequence sites, features and motifs" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [ "Thornton Tools", "EBI Tools" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "http://www.ebi.ac.uk/about/terms-of-use", "type": [ "Terms of use" ], "note": null }, { "url": "http://www.ebi.ac.uk/thornton-srv/databases/sas", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/protein/11.10.855", "pmid": "9862203", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Roman Laskowski", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Thornton Group", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Duncan Milburn", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Contributor" ], "note": null }, { "name": "EMBL-EBI", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": null, "email": "roman@ebi.ac.uk", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Roman Laskowski", "email": "roman@ebi.ac.uk", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "EMBL-EBI", "additionDate": "2015-01-29T15:47:21Z", "lastUpdate": "2024-11-25T15:57:26.863506Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "leBIBIpqp", "description": "The BioInformatics Prokaryotes Quick Phylogeny is designed to reconstruct the phylogeny of an Archaea or a Bacteria from its nucleic acid sequence. It is also giving the useful informations if species identification is needed.", "homepage": "https://umr5558-bibiserv.univ-lyon1.fr/lebibi/lebibi.cgi", "biotoolsID": "lebibipqp", "biotoolsCURIE": "biotools:lebibipqp", "version": [ "6.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0567", "term": "Phylogenetic tree visualisation" }, { "uri": "http://edamontology.org/operation_0258", "term": "Sequence alignment analysis" }, { "uri": "http://edamontology.org/operation_0338", "term": "Sequence database search" }, { "uri": "http://edamontology.org/operation_0292", "term": "Sequence alignment" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2044", "term": "Sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_1056", "term": "Database name" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_1984", "term": "FASTA-aln" } ] }, { "data": { "uri": "http://edamontology.org/data_2048", "term": "Report" }, "format": [ { "uri": "http://edamontology.org/format_2331", "term": "HTML" } ] }, { "data": { "uri": "http://edamontology.org/data_3272", "term": "Species tree" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_0857", "term": "Sequence search results" }, "format": [ { "uri": "http://edamontology.org/format_1333", "term": "BLAST results" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0084", "term": "Phylogeny" }, { "uri": "http://edamontology.org/topic_0621", "term": "Model organisms" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://umr5558-bibiserv.univ-lyon1.fr/BIBIDOCNEW/index.html#lebibi-qbpp-documentation", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1186/s12859-015-0692-z", "pmid": "26264559", "pmcid": "PMC4531848", "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "IFB ELIXIR-FR", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Jean-Pierre Flandrois", "email": "jean-pierre.flandrois@univ-lyon1.fr", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "ELIXIR-FR", "additionDate": "2015-01-22T11:28:32Z", "lastUpdate": "2024-11-25T15:53:39.526130Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "SeaView", "description": "Multiplatform graphical user interface designed to facilitate alignment and phylogenic tree building from molecular sequences.", "homepage": "http://doua.prabi.fr/software/seaview", "biotoolsID": "seaview", "biotoolsCURIE": "biotools:seaview", "version": [ "4" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0567", "term": "Phylogenetic tree visualisation" }, { "uri": "http://edamontology.org/operation_0564", "term": "Sequence visualisation" }, { "uri": "http://edamontology.org/operation_0326", "term": "Phylogenetic tree editing" }, { "uri": "http://edamontology.org/operation_0492", "term": "Multiple sequence alignment" }, { "uri": "http://edamontology.org/operation_0540", "term": "Phylogenetic tree generation (from molecular sequences)" }, { "uri": "http://edamontology.org/operation_3081", "term": "Sequence alignment editing" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2044", "term": "Sequence" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_0872", "term": "Phylogenetic tree" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0872", "term": "Phylogenetic tree" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1707", "term": "Phylogenetic tree image" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1711", "term": "Sequence alignment image" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool", "Desktop application" ], "topic": [ { "uri": "http://edamontology.org/topic_0092", "term": "Data visualisation" }, { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/topic_0084", "term": "Phylogeny" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "http://doua.prabi.fr/software/seaview", "type": [ "Software catalogue" ], "note": null } ], "download": [], "documentation": [ { "url": "http://doua.prabi.fr/main/index", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/molbev/msp259", "pmid": "19854763", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "IFB ELIXIR-FR", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Manolo Gouy", "email": "mgouy@biomserv.uni-lyon1.fr", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "ELIXIR-FR", "additionDate": "2015-01-22T11:28:31Z", "lastUpdate": "2024-11-25T15:49:59.006607Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "SWIPE", "description": "Tool for performing rapid local alignment searches in amino acid or nucleotide sequence databases. It is a highly optimized implementation of the Smith-Waterman algoritm using SIMD parallel computing technology available on common CPUs.", "homepage": "http://dna.uio.no/swipe", "biotoolsID": "swipe", "biotoolsCURIE": "biotools:swipe", "version": [ "2.0.5" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0292", "term": "Sequence alignment" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2976", "term": "Protein sequence" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2977", "term": "Nucleic acid sequence" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1383", "term": "Sequence alignment (nucleic acid)" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1384", "term": "Sequence alignment (protein)" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/topic_3047", "term": "Molecular biology" } ], "operatingSystem": [ "Linux" ], "language": [ "C++" ], "license": "AGPL-3.0", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/torognes/swipe", "type": [ "Repository" ], "note": null } ], "download": [ { "url": "https://github.com/torognes/swipe", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-12-221", "type": [ "Citation instructions" ], "note": null }, { "url": "http://dna.uio.no/swipe/", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1186/1471-2105-12-221", "pmid": "21631914", "pmcid": "PMC3120707", "type": [ "Primary" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Torbjørn Rognes", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "UiO", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": null, "email": "torognes@ifi.uio.no", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "UiO", "additionDate": "2016-03-07T13:27:05Z", "lastUpdate": "2024-11-25T15:40:47.660414Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "rnaSeqMap", "description": "A library provides classes and functions to analyze the RNA-sequencing data using the coverage profiles in multiple samples at a time.", "homepage": "http://bioconductor.org/packages/release/bioc/html/rnaSeqMap.html", "biotoolsID": "rnaseqmap", "biotoolsCURIE": "biotools:rnaseqmap", "version": [ "2.32.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3680", "term": "RNA-Seq analysis" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1383", "term": "Sequence alignment (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_2572", "term": "BAM" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_1921", "term": "Alignment format" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool", "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_3170", "term": "RNA-Seq" }, { "uri": "http://edamontology.org/topic_0203", "term": "Gene expression" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "R" ], "license": "GPL-2.0", "collectionID": [ "BioConductor" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "http://bioconductor/packages/release/bioc/src/contrib/rnaSeqMap_2.32.0.tar.gz", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "http://bioconductor.org/packages/release/bioc/html/rnaSeqMap.html", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1186/1471-2105-12-200", "pmid": "21612622", "pmcid": "PMC3128033", "type": [ "Primary" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Michal Okoniewski", "email": "michal@fgcz.ethz.ch", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "bioconductor_import", "additionDate": "2017-01-17T14:58:34Z", "lastUpdate": "2024-11-25T15:31:04.406293Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "BSgenome", "description": "Infrastructure shared by all the Biostrings-based genome data packages.", "homepage": "http://bioconductor.org/packages/release/bioc/html/BSgenome.html", "biotoolsID": "bsgenome", "biotoolsCURIE": "biotools:bsgenome", "version": [ "1.42.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_1812", "term": "Loading" }, { "uri": "http://edamontology.org/operation_2403", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/operation_0368", "term": "Sequence masking" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0849", "term": "Sequence record" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" }, { "uri": "http://edamontology.org/format_1919", "term": "Sequence record format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0849", "term": "Sequence record" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] }, { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool", "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/topic_3071", "term": "Data management" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "R" ], "license": "Artistic-2.0", "collectionID": [ "BioConductor" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "http://bioconductor/packages/release/bioc/src/contrib/BSgenome_1.42.0.tar.gz", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "http://bioconductor.org/packages/release/bioc/html/BSgenome.html", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1038/nmeth.3252", "pmid": "25633503", "pmcid": "PMC4509590", "type": [ "Other" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "H. Pagès", "email": "hpages@fredhutch.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "bioconductor_import", "additionDate": "2017-01-17T14:58:01Z", "lastUpdate": "2024-11-25T15:30:28.305550Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Rbowtie", "description": "This package provides an R wrapper around the popular bowtie short read aligner and around SpliceMap, a de novo splice junction discovery and alignment tool. The package is used by the QuasR bioconductor package. We recommend to use QuasR instead of using this package directly.", "homepage": "http://bioconductor.org/packages/release/bioc/html/Rbowtie.html", "biotoolsID": "rbowtie", "biotoolsCURIE": "biotools:rbowtie", "version": [ "1.14.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0433", "term": "Splice site prediction" }, { "uri": "http://edamontology.org/operation_3198", "term": "Read mapping" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1383", "term": "Sequence alignment (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_1957", "term": "raw" }, { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" }, { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0867", "term": "Sequence alignment report" }, "format": [ { "uri": "http://edamontology.org/format_2573", "term": "SAM" } ] }, { "data": { "uri": "http://edamontology.org/data_1383", "term": "Sequence alignment (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_2573", "term": "SAM" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool", "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_3168", "term": "Sequencing" }, { "uri": "http://edamontology.org/topic_3053", "term": "Genetics" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": "Artistic-1.0", "collectionID": [ "BioConductor" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "http://bioconductor/packages/release/bioc/src/contrib/Rbowtie_1.14.0.tar.gz", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "http://bioconductor.org/packages/release/bioc/html/Rbowtie.html", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1038/nmeth.3252", "pmid": "25633503", "pmcid": "PMC4509590", "type": [ "Other" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Michael Stadler", "email": "michael.stadler@fmi.ch", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "bioconductor_import", "additionDate": "2017-01-17T14:57:43Z", "lastUpdate": "2024-11-25T15:29:52.166738Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "gmapR", "description": "GSNAP and GMAP are a pair of tools to align short-read data. This package provides convenience methods to work with GMAP and GSNAP from within R. In addition, it provides methods to tally alignment results on a per-nucleotide basis using the bam_tally tool.", "homepage": "http://bioconductor.org/packages/release/bioc/html/gmapR.html", "biotoolsID": "gmapr", "biotoolsCURIE": "biotools:gmapr", "version": [ "1.16.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2478", "term": "Nucleic acid sequence analysis" }, { "uri": "http://edamontology.org/operation_3198", "term": "Read mapping" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0849", "term": "Sequence record" }, "format": [ { "uri": "http://edamontology.org/format_2572", "term": "BAM" }, { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" }, { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_1383", "term": "Sequence alignment (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_2572", "term": "BAM" }, { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" }, { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1383", "term": "Sequence alignment (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_2572", "term": "BAM" }, { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] }, { "data": { "uri": "http://edamontology.org/data_0867", "term": "Sequence alignment report" }, "format": [ { "uri": "http://edamontology.org/format_2572", "term": "BAM" }, { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] }, { "data": { "uri": "http://edamontology.org/data_1276", "term": "Nucleic acid features" }, "format": [ { "uri": "http://edamontology.org/format_2572", "term": "BAM" }, { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool", "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_0102", "term": "Mapping" }, { "uri": "http://edamontology.org/topic_3170", "term": "RNA-Seq" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "R" ], "license": "Artistic-2.0", "collectionID": [ "BioConductor" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "http://bioconductor/packages/release/bioc/src/contrib/gmapR_1.16.0.tar.gz", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "http://bioconductor.org/packages/release/bioc/html/gmapR.html", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1007/978-1-4939-3578-9_15", "pmid": "27008021", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Michael Lawrence", "email": "lawrence.michael@gene.com", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "bioconductor_import", "additionDate": "2017-01-17T14:57:33Z", "lastUpdate": "2024-11-25T15:29:46.206228Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "BBCAnalyzer", "description": "This package visualizes the relative or absolute number of bases, deletions and insertions at defined positions in sequence alignment data available as bam files in comparison to the reference bases. Markers for the relative base frequencies, the mean quality of the detected bases, known mutations or polymorphisms and variants called in the data may additionally be included in the plots.", "homepage": "http://bioconductor.org/packages/release/bioc/html/BBCAnalyzer.html", "biotoolsID": "bbcanalyzer", "biotoolsCURIE": "biotools:bbcanalyzer", "version": [ "1.4.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0564", "term": "Sequence visualisation" }, { "uri": "http://edamontology.org/operation_2478", "term": "Nucleic acid sequence analysis" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1383", "term": "Sequence alignment (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_2572", "term": "BAM" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1383", "term": "Sequence alignment (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_1921", "term": "Alignment format" }, { "uri": "http://edamontology.org/format_2921", "term": "Sequence variation annotation format" } ] }, { "data": { "uri": "http://edamontology.org/data_2166", "term": "Sequence composition plot" }, "format": [ { "uri": "http://edamontology.org/format_1921", "term": "Alignment format" }, { "uri": "http://edamontology.org/format_2921", "term": "Sequence variation annotation format" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool", "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/topic_0092", "term": "Data visualisation" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "R" ], "license": "GPL-3.0", "collectionID": [ "BioConductor" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "http://bioconductor/packages/release/bioc/src/contrib/BBCAnalyzer_1.4.0.tar.gz", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "http://bioconductor.org/packages/release/bioc/html/BBCAnalyzer.html", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1186/s12859-017-1549-4", "pmid": "28241736", "pmcid": "PMC5330023", "type": [ "Primary" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Sarah Sandmann", "email": "sarah.sandmann@uni-muenster.de", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "bioconductor_import", "additionDate": "2017-01-17T14:57:28Z", "lastUpdate": "2024-11-25T15:29:44.588777Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "bamsignals", "description": "This package allows to efficiently obtain count vectors from indexed bam files. It counts the number of reads in given genomic ranges and it computes reads profiles and coverage profiles. It also handles paired-end data.", "homepage": "http://bioconductor.org/packages/release/bioc/html/bamsignals.html", "biotoolsID": "bamsignals", "biotoolsCURIE": "biotools:bamsignals", "version": [ "1.6.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2478", "term": "Nucleic acid sequence analysis" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1383", "term": "Sequence alignment (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_2572", "term": "BAM" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0867", "term": "Sequence alignment report" }, "format": [ { "uri": "http://edamontology.org/format_1921", "term": "Alignment format" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool", "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/topic_0092", "term": "Data visualisation" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "R" ], "license": "GPL-2.0", "collectionID": [ "BioConductor" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "http://bioconductor/packages/release/bioc/src/contrib/bamsignals_1.6.0.tar.gz", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "http://bioconductor.org/packages/release/bioc/html/bamsignals.html", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1038/nmeth.3252", "pmid": "25633503", "pmcid": "PMC4509590", "type": [ "Other" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Alessandro Mammana", "email": "mammana@molgen.mpg.de", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "bioconductor_import", "additionDate": "2017-01-17T14:57:28Z", "lastUpdate": "2024-11-25T15:29:43.173812Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "BaseSpaceR", "description": "A rich R interface to Illumina's BaseSpace cloud computing environment, enabling the fast development of data analysis and visualisation tools.", "homepage": "http://bioconductor.org/packages/release/bioc/html/BaseSpaceR.html", "biotoolsID": "basespacer", "biotoolsCURIE": "biotools:basespacer", "version": [ "1.18.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0564", "term": "Sequence visualisation" }, { "uri": "http://edamontology.org/operation_2478", "term": "Nucleic acid sequence analysis" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0849", "term": "Sequence record" }, "format": [ { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1383", "term": "Sequence alignment (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_2572", "term": "BAM" }, { "uri": "http://edamontology.org/format_3016", "term": "VCF" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool", "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/topic_0092", "term": "Data visualisation" }, { "uri": "http://edamontology.org/topic_3372", "term": "Software engineering" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "R" ], "license": "Apache-2.0", "collectionID": [ "BioConductor" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "http://bioconductor/packages/release/bioc/src/contrib/BaseSpaceR_1.18.0.tar.gz", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "http://bioconductor.org/packages/release/bioc/html/BaseSpaceR.html", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1038/nmeth.3252", "pmid": "25633503", "pmcid": "PMC4509590", "type": [ "Other" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Jared O'Connell", "email": "joconnell@illumina.com", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "bioconductor_import", "additionDate": "2017-01-17T14:55:06Z", "lastUpdate": "2024-11-25T15:27:20.876397Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "UniProt Align", "description": "Multiple sequence alignment.", "homepage": "http://www.uniprot.org/align", "biotoolsID": "uniprot_align", "biotoolsCURIE": "biotools:uniprot_align", "version": [ "1" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0492", "term": "Multiple sequence alignment" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2976", "term": "Protein sequence" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": "CC-BY-ND-3.0", "collectionID": [ "UniProt Tools", "EBI Tools" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "http://www.uniprot.org/contact", "type": [ "Helpdesk" ], "note": null } ], "download": [], "documentation": [ { "url": "http://www.ebi.ac.uk/about/terms-of-use", "type": [ "Terms of use" ], "note": null }, { "url": "http://www.uniprot.org/help/sequence-alignments", "type": [ "General" ], "note": null }, { "url": "http://www.uniprot.org/help/license", "type": [ "Terms of use" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gku989", "pmid": "25348405", "pmcid": "PMC4384041", "type": [ "Primary" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "UniProt Consortium", "email": null, "url": "http://www.uniprot.org/help/about", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "EMBL-EBI", "email": null, "url": "http://www.ebi.ac.uk/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": null, "email": null, "url": "http://www.uniprot.org/contact", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Xavier Watkins", "email": "watkins@ebi.ac.uk", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "EMBL-EBI", "additionDate": "2015-01-29T15:47:38Z", "lastUpdate": "2024-11-25T15:19:23.003433Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Picky", "description": "A pipeline for detecting structural variants from third generation long read sequencing data (works on Oxford Nanopore and PacBio).", "homepage": "https://github.com/TheJacksonLaboratory/Picky", "biotoolsID": "picky", "biotoolsCURIE": "biotools:picky", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0253", "term": "Sequence feature detection" }, { "uri": "http://edamontology.org/operation_0292", "term": "Sequence alignment" }, { "uri": "http://edamontology.org/operation_3228", "term": "Structural variation detection" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3497", "term": "DNA sequence (raw)" }, "format": [ { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" } ] }, { "data": { "uri": "http://edamontology.org/data_2093", "term": "Data reference" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1383", "term": "Sequence alignment (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_2573", "term": "SAM" } ] }, { "data": { "uri": "http://edamontology.org/data_3498", "term": "Sequence variations" }, "format": [ { "uri": "http://edamontology.org/format_3016", "term": "VCF" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3168", "term": "Sequencing" }, { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/topic_0199", "term": "Genetic variation" }, { "uri": "http://edamontology.org/topic_0769", "term": "Workflows" }, { "uri": "http://edamontology.org/topic_2640", "term": "Oncology" } ], "operatingSystem": [ "Linux", "Mac" ], "language": [ "Perl" ], "license": null, "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "https://github.com/TheJacksonLaboratory/Picky", "type": "Software package", "note": "A Github page.", "version": null } ], "documentation": [ { "url": "https://github.com/TheJacksonLaboratory/Picky/wiki", "type": [ "General" ], "note": "A Github wiki" } ], "publication": [ { "doi": "10.1038/s41592-018-0002-6", "pmid": "29713081", "pmcid": "PMC5990454", "type": [], "version": null, "note": null, "metadata": { "title": "Picky comprehensively detects high-resolution structural variants in nanopore long reads", "abstract": "Acquired genomic structural variants (SVs) are major hallmarks of cancer genomes, but they are challenging to reconstruct from short-read sequencing data. Here we exploited the long reads of the nanopore platform using our customized pipeline, Picky (https://github.com/TheJacksonLaboratory/Picky) to reveal SVs of diverse architecture in a breast cancer model. We identified the full spectrum of SVs with superior specificity and sensitivity relative to short-read analyses, and uncovered repetitive DNA as the major source of variation. Examination of genome-wide breakpoints at nucleotide resolution uncovered micro-insertions as the common structural features associated with SVs. Breakpoint density across the genome is associated with the propensity for interchromosomal connectivity and was found to be enriched in promoters and transcribed regions of the genome. Furthermore, we observed an over-representation of reciprocal translocations from chromosomal double-crossovers through phased SVs. We demonstrate that Picky analysis is an effective tool for comprehensive detection of SVs in cancer genomes from long-read data.", "date": "2018-06-01T00:00:00Z", "citationCount": 70, "authors": [ { "name": "Gong L." }, { "name": "Wong C.-H." }, { "name": "Cheng W.-C." }, { "name": "Tjong H." }, { "name": "Menghi F." }, { "name": "Ngan C.Y." }, { "name": "Liu E.T." }, { "name": "Wei C.-L." } ], "journal": "Nature Methods" } } ], "credit": [ { "name": "Chia-Lin Wei", "email": null, "url": "https://www.nature.com/articles/s41592-018-0002-6/email/correspondent/c1/new", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "ELIXIR-EE", "additionDate": "2018-05-15T16:14:12Z", "lastUpdate": "2024-11-25T14:49:38.684177Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "cellAlign", "description": "A method for comparing expression dynamics within and between single-cell differentiation trajectories.", "homepage": "https://github.com/shenorrLab/cellAlign", "biotoolsID": "cellalign", "biotoolsCURIE": "biotools:cellalign", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3439", "term": "Pathway or network prediction" }, { "uri": "http://edamontology.org/operation_3223", "term": "Differential gene expression analysis" }, { "uri": "http://edamontology.org/operation_0314", "term": "Gene expression profiling" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3112", "term": "Gene expression matrix" }, "format": [ { "uri": "http://edamontology.org/format_3033", "term": "Matrix format" } ] }, { "data": { "uri": "http://edamontology.org/data_2337", "term": "Resource metadata" }, "format": [ { "uri": "http://edamontology.org/format_3326", "term": "Data index format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0867", "term": "Sequence alignment report" }, "format": [ { "uri": "http://edamontology.org/format_2032", "term": "Workflow format" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Plug-in" ], "topic": [ { "uri": "http://edamontology.org/topic_0203", "term": "Gene expression" }, { "uri": "http://edamontology.org/topic_2229", "term": "Cell biology" }, { "uri": "http://edamontology.org/topic_3064", "term": "Developmental biology" } ], "operatingSystem": [ "Windows" ], "language": [ "R" ], "license": "Other", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "https://github.com/shenorrLab/cellAlign", "type": "Software package", "note": null, "version": null } ], "documentation": [ { "url": "https://github.com/shenorrLab/cellAlign", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1038/nmeth.4628", "pmid": "29529018", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Alignment of single-cell trajectories to compare cellular expression dynamics", "abstract": "Single-cell RNA sequencing and high-dimensional cytometry can be used to generate detailed trajectories of dynamic biological processes such as differentiation or development. Here we present cellAlign, a quantitative framework for comparing expression dynamics within and between single-cell trajectories. By applying cellAlign to mouse and human embryonic developmental trajectories, we systematically delineate differences in the temporal regulation of gene expression programs that would otherwise be masked.", "date": "2018-04-03T00:00:00Z", "citationCount": 55, "authors": [ { "name": "Alpert A." }, { "name": "Moore L.S." }, { "name": "Dubovik T." }, { "name": "Shen-Orr S.S." } ], "journal": "Nature Methods" } } ], "credit": [ { "name": "Ayelet Alpert", "email": null, "url": "https://www.linkedin.com/in/ayelet-alpert-5a525167/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "ELIXIR-EE", "additionDate": "2018-05-29T14:26:15Z", "lastUpdate": "2024-11-25T14:35:34.209960Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Biostrings", "description": "Memory efficient string containers, string matching algorithms, and other utilities, for fast manipulation of large biological sequences or sets of sequences.", "homepage": "http://bioconductor.org/packages/release/bioc/html/Biostrings.html", "biotoolsID": "biostrings", "biotoolsCURIE": "biotools:biostrings", "version": [ "2.42.1" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_1812", "term": "Loading" }, { "uri": "http://edamontology.org/operation_2403", "term": "Sequence analysis" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3115", "term": "Microarray metadata" }, "format": [ { "uri": "http://edamontology.org/format_2061", "term": "Nucleic acid features (primers) format" }, { "uri": "http://edamontology.org/format_2554", "term": "Alignment format (text)" }, { "uri": "http://edamontology.org/format_1919", "term": "Sequence record format" } ] }, { "data": { "uri": "http://edamontology.org/data_0849", "term": "Sequence record" }, "format": [ { "uri": "http://edamontology.org/format_2061", "term": "Nucleic acid features (primers) format" }, { "uri": "http://edamontology.org/format_2554", "term": "Alignment format (text)" }, { "uri": "http://edamontology.org/format_1919", "term": "Sequence record format" } ] }, { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_2061", "term": "Nucleic acid features (primers) format" }, { "uri": "http://edamontology.org/format_2554", "term": "Alignment format (text)" }, { "uri": "http://edamontology.org/format_1919", "term": "Sequence record format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3115", "term": "Microarray metadata" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] }, { "data": { "uri": "http://edamontology.org/data_0849", "term": "Sequence record" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] }, { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool", "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/topic_3071", "term": "Data management" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "R" ], "license": "Artistic-2.0", "collectionID": [ "BioConductor" ], "maturity": null, "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "http://bioconductor/packages/release/bioc/src/contrib/Biostrings_2.42.1.tar.gz", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "http://bioconductor.org/packages/release/bioc/html/Biostrings.html", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1038/nmeth.3252", "pmid": "25633503", "pmcid": "PMC4509590", "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "Orchestrating high-throughput genomic analysis with Bioconductor", "abstract": "Bioconductor is an open-source, open-development software project for the analysis and comprehension of high-throughput data in genomics and molecular biology. The project aims to enable interdisciplinary research, collaboration and rapid development of scientific software. Based on the statistical programming language R, Bioconductor comprises 934 interoperable packages contributed by a large, diverse community of scientists. Packages cover a range of bioinformatic and statistical applications. They undergo formal initial review and continuous automated testing. We present an overview for prospective users and contributors.", "date": "2015-01-01T00:00:00Z", "citationCount": 2315, "authors": [ { "name": "Huber W." }, { "name": "Carey V.J." }, { "name": "Gentleman R." }, { "name": "Anders S." }, { "name": "Carlson M." }, { "name": "Carvalho B.S." }, { "name": "Bravo H.C." }, { "name": "Davis S." }, { "name": "Gatto L." }, { "name": "Girke T." }, { "name": "Gottardo R." }, { "name": "Hahne F." }, { "name": "Hansen K.D." }, { "name": "Irizarry R.A." }, { "name": "Lawrence M." }, { "name": "Love M.I." }, { "name": "MaCdonald J." }, { "name": "Obenchain V." }, { "name": "Oles A.K." }, { "name": "Pages H." }, { "name": "Reyes A." }, { "name": "Shannon P." }, { "name": "Smyth G.K." }, { "name": "Tenenbaum D." }, { "name": "Waldron L." }, { "name": "Morgan M." } ], "journal": "Nature Methods" } } ], "credit": [ { "name": "H. Pagès", "email": "hpages@fredhutch.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "bioconductor_import", "additionDate": "2017-01-17T14:57:29Z", "lastUpdate": "2024-11-25T14:35:14.288041Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Phymyco-DB", "description": "A database designed to help the mycologist community to access to fungal DNA markers data for phylogenetic analyses.", "homepage": "http://phymycodb.genouest.org/", "biotoolsID": "phymyco-db", "biotoolsCURIE": "biotools:phymyco-db", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2928", "term": "Alignment" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2977", "term": "Nucleic acid sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "note": "Sequence alignment", "cmd": null } ], "toolType": [ "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_0623", "term": "Gene and protein families" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "http://phymycodb.genouest.org/", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1371/journal.pone.0043117", "pmid": "23028445", "pmcid": "PMC3441585", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "PHYMYCO-DB: A Curated Database for Analyses of Fungal Diversity and Evolution", "abstract": "Background: In environmental sequencing studies, fungi can be identified based on nucleic acid sequences, using either highly variable sequences as species barcodes or conserved sequences containing a high-quality phylogenetic signal. For the latter, identification relies on phylogenetic analyses and the adoption of the phylogenetic species concept. Such analysis requires that the reference sequences are well identified and deposited in public-access databases. However, many entries in the public sequence databases are problematic in terms of quality and reliability and these data require screening to ensure correct phylogenetic interpretation. Methods and Principal Findings: To facilitate phylogenetic inferences and phylogenetic assignment, we introduce a fungal sequence database. The database PHYMYCO-DB comprises fungal sequences from GenBank that have been filtered to satisfy stringent sequence quality criteria. For the first release, two widely used molecular taxonomic markers were chosen: the nuclear SSU rRNA and EF1-α gene sequences. Following the automatic extraction and filtration, a manual curation is performed to remove problematic sequences while preserving relevant sequences useful for phylogenetic studies. As a result of curation, ~20% of the automatically filtered sequences have been removed from the database. To demonstrate how PHYMYCO-DB can be employed, we test a set of environmental Chytridiomycota sequences obtained from deep sea samples. Conclusion: PHYMYCO-DB offers the tools necessary to: (i) extract high quality fungal sequences for each of the 5 fungal phyla, at all taxonomic levels, (ii) extract already performed alignments, to act as 'reference alignments', (iii) launch alignments of personal sequences along with stored data. A total of 9120 SSU rRNA and 672 EF1-α high-quality fungal sequences are now available. The PHYMYCO-DB is accessible through the URL http://phymycodb.genouest.org. © 2012 Mahé et al.", "date": "2012-09-13T00:00:00Z", "citationCount": 37, "authors": [ { "name": "Mahe S." }, { "name": "Duhamel M." }, { "name": "Le Calvez T." }, { "name": "Guillot L." }, { "name": "Sarbu L." }, { "name": "Bretaudeau A." }, { "name": "Collin O." }, { "name": "Dufresne A." }, { "name": "Kiers E.T." }, { "name": "Vandenkoornhuyse P." } ], "journal": "PLoS ONE" } } ], "credit": [ { "name": "GenOuest", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "GenOuest", "email": "support@genouest.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "GenOuest", "additionDate": "2015-01-21T15:12:26Z", "lastUpdate": "2024-11-25T14:25:53.229148Z", "editPermission": { "type": "group", "authors": [ "olivier.collin@irisa.fr" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Ensembl Genomes Fungi sequence search", "description": "Searches Ensembl Fungi sequences using Exonerate.", "homepage": "http://fungi.ensembl.org/Multi/enasearch", "biotoolsID": "ensembl_genomes_fungi_sequence_search", "biotoolsCURIE": "biotools:ensembl_genomes_fungi_sequence_search", "version": [ "1" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0346", "term": "Sequence similarity search" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2044", "term": "Sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_0857", "term": "Sequence search results" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [ "Ensembl Tools", "Ensembl Genomes", "EBI Tools" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "http://www.ebi.ac.uk/about/terms-of-use", "type": [ "Terms of use" ], "note": null }, { "url": "http://fungi.ensembl.org/info/website/help/index.html", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gkv1157", "pmid": "26687719", "pmcid": "PMC4702834", "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "Ensembl 2016", "abstract": "The Ensembl project (http://www.ensembl.org) is a system for genome annotation, analysis, storage and dissemination designed to facilitate the access of genomic annotation from chordates and key model organisms. It provides access to data from 87 species across our main and early access Pre! websites. This year we introduced three newly annotated species and released numerous updates across our supported species with a concentration on data for the latest genome assemblies of human, mouse, zebrafish and rat. We also provided two data updates for the previous human assembly, GRCh37, through a dedicated website (http://grch37.ensembl.org) Our tools, in particular the VEP, have been improved significantly through integration of additional third party data. REST is now capable of larger-scale analysis and our regulatory data BioMart can deliver faster results. The website is now capable of displaying long-range interactions such as those found in cis-regulated datasets. Finally we have launched a website optimized for mobile devices providing views of genes, variants and phenotypes. Our data is made available without restriction and all code is available from our GitHub organization site (http://github.com/Ensembl) under an Apache 2.0 license.", "date": "2016-01-01T00:00:00Z", "citationCount": 1097, "authors": [ { "name": "Yates A." }, { "name": "Akanni W." }, { "name": "Amode M.R." }, { "name": "Barrell D." }, { "name": "Billis K." }, { "name": "Carvalho-Silva D." }, { "name": "Cummins C." }, { "name": "Clapham P." }, { "name": "Fitzgerald S." }, { "name": "Gil L." }, { "name": "Giron C.G." }, { "name": "Gordon L." }, { "name": "Hourlier T." }, { "name": "Hunt S.E." }, { "name": "Janacek S.H." }, { "name": "Johnson N." }, { "name": "Juettemann T." }, { "name": "Keenan S." }, { "name": "Lavidas I." }, { "name": "Martin F.J." }, { "name": "Maurel T." }, { "name": "McLaren W." }, { "name": "Murphy D.N." }, { "name": "Nag R." }, { "name": "Nuhn M." }, { "name": "Parker A." }, { "name": "Patricio M." }, { "name": "Pignatelli M." }, { "name": "Rahtz M." }, { "name": "Riat H.S." }, { "name": "Sheppard D." }, { "name": "Taylor K." }, { "name": "Thormann A." }, { "name": "Vullo A." }, { "name": "Wilder S.P." }, { "name": "Zadissa A." }, { "name": "Birney E." }, { "name": "Harrow J." }, { "name": "Muffato M." }, { "name": "Perry E." }, { "name": "Ruffier M." }, { "name": "Spudich G." }, { "name": "Trevanion S.J." }, { "name": "Cunningham F." }, { "name": "Aken B.L." }, { "name": "Zerbino D.R." }, { "name": "Flicek P." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "Ensembl team", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "EMBL-EBI", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": null, "email": "helpdesk@ensemblgenomes.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Ensembl Genomes webteam", "email": "eg-webteam@ebi.ac.uk", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "EMBL-EBI", "additionDate": "2015-01-29T15:47:57Z", "lastUpdate": "2024-11-25T14:21:53.634324Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Ensembl Genomes Protists sequence search", "description": "Searches Ensembl Protists sequences using Exonerate.", "homepage": "http://protists.ensembl.org/Multi/enasearch", "biotoolsID": "ensembl_genomes_protists_sequence_search", "biotoolsCURIE": "biotools:ensembl_genomes_protists_sequence_search", "version": [ "1" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0346", "term": "Sequence similarity search" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2044", "term": "Sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [ "Ensembl Tools", "Ensembl Genomes", "EBI Tools" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "http://www.ebi.ac.uk/about/terms-of-use", "type": [ "Terms of use" ], "note": null }, { "url": "http://protists.ensembl.org/info/website/help/index.html", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gkv1157", "pmid": "26687719", "pmcid": "PMC4702834", "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "Ensembl 2016", "abstract": "The Ensembl project (http://www.ensembl.org) is a system for genome annotation, analysis, storage and dissemination designed to facilitate the access of genomic annotation from chordates and key model organisms. It provides access to data from 87 species across our main and early access Pre! websites. This year we introduced three newly annotated species and released numerous updates across our supported species with a concentration on data for the latest genome assemblies of human, mouse, zebrafish and rat. We also provided two data updates for the previous human assembly, GRCh37, through a dedicated website (http://grch37.ensembl.org) Our tools, in particular the VEP, have been improved significantly through integration of additional third party data. REST is now capable of larger-scale analysis and our regulatory data BioMart can deliver faster results. The website is now capable of displaying long-range interactions such as those found in cis-regulated datasets. Finally we have launched a website optimized for mobile devices providing views of genes, variants and phenotypes. Our data is made available without restriction and all code is available from our GitHub organization site (http://github.com/Ensembl) under an Apache 2.0 license.", "date": "2016-01-01T00:00:00Z", "citationCount": 1097, "authors": [ { "name": "Yates A." }, { "name": "Akanni W." }, { "name": "Amode M.R." }, { "name": "Barrell D." }, { "name": "Billis K." }, { "name": "Carvalho-Silva D." }, { "name": "Cummins C." }, { "name": "Clapham P." }, { "name": "Fitzgerald S." }, { "name": "Gil L." }, { "name": "Giron C.G." }, { "name": "Gordon L." }, { "name": "Hourlier T." }, { "name": "Hunt S.E." }, { "name": "Janacek S.H." }, { "name": "Johnson N." }, { "name": "Juettemann T." }, { "name": "Keenan S." }, { "name": "Lavidas I." }, { "name": "Martin F.J." }, { "name": "Maurel T." }, { "name": "McLaren W." }, { "name": "Murphy D.N." }, { "name": "Nag R." }, { "name": "Nuhn M." }, { "name": "Parker A." }, { "name": "Patricio M." }, { "name": "Pignatelli M." }, { "name": "Rahtz M." }, { "name": "Riat H.S." }, { "name": "Sheppard D." }, { "name": "Taylor K." }, { "name": "Thormann A." }, { "name": "Vullo A." }, { "name": "Wilder S.P." }, { "name": "Zadissa A." }, { "name": "Birney E." }, { "name": "Harrow J." }, { "name": "Muffato M." }, { "name": "Perry E." }, { "name": "Ruffier M." }, { "name": "Spudich G." }, { "name": "Trevanion S.J." }, { "name": "Cunningham F." }, { "name": "Aken B.L." }, { "name": "Zerbino D.R." }, { "name": "Flicek P." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "Ensembl team", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "EMBL-EBI", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": null, "email": "helpdesk@ensemblgenomes.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Ensembl Genomes webteam", "email": "eg-webteam@ebi.ac.uk", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "EMBL-EBI", "additionDate": "2015-01-29T15:47:49Z", "lastUpdate": "2024-11-25T14:21:52.233955Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Ensembl Genomes Metazoa sequence search", "description": "Searches Ensembl Metazoa sequences using Exonerate.", "homepage": "http://metazoa.ensembl.org/Multi/enasearch", "biotoolsID": "ensembl_genomes_metazoa_sequence_search", "biotoolsCURIE": "biotools:ensembl_genomes_metazoa_sequence_search", "version": [ "1" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0346", "term": "Sequence similarity search" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2044", "term": "Sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [ "Ensembl Tools", "Ensembl Genomes", "EBI Tools" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "http://www.ebi.ac.uk/about/terms-of-use", "type": [ "Terms of use" ], "note": null }, { "url": "http://metazoa.ensembl.org/info/website/help/index.html", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gkv1157", "pmid": "26687719", "pmcid": "PMC4702834", "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "Ensembl 2016", "abstract": "The Ensembl project (http://www.ensembl.org) is a system for genome annotation, analysis, storage and dissemination designed to facilitate the access of genomic annotation from chordates and key model organisms. It provides access to data from 87 species across our main and early access Pre! websites. This year we introduced three newly annotated species and released numerous updates across our supported species with a concentration on data for the latest genome assemblies of human, mouse, zebrafish and rat. We also provided two data updates for the previous human assembly, GRCh37, through a dedicated website (http://grch37.ensembl.org) Our tools, in particular the VEP, have been improved significantly through integration of additional third party data. REST is now capable of larger-scale analysis and our regulatory data BioMart can deliver faster results. The website is now capable of displaying long-range interactions such as those found in cis-regulated datasets. Finally we have launched a website optimized for mobile devices providing views of genes, variants and phenotypes. Our data is made available without restriction and all code is available from our GitHub organization site (http://github.com/Ensembl) under an Apache 2.0 license.", "date": "2016-01-01T00:00:00Z", "citationCount": 1097, "authors": [ { "name": "Yates A." }, { "name": "Akanni W." }, { "name": "Amode M.R." }, { "name": "Barrell D." }, { "name": "Billis K." }, { "name": "Carvalho-Silva D." }, { "name": "Cummins C." }, { "name": "Clapham P." }, { "name": "Fitzgerald S." }, { "name": "Gil L." }, { "name": "Giron C.G." }, { "name": "Gordon L." }, { "name": "Hourlier T." }, { "name": "Hunt S.E." }, { "name": "Janacek S.H." }, { "name": "Johnson N." }, { "name": "Juettemann T." }, { "name": "Keenan S." }, { "name": "Lavidas I." }, { "name": "Martin F.J." }, { "name": "Maurel T." }, { "name": "McLaren W." }, { "name": "Murphy D.N." }, { "name": "Nag R." }, { "name": "Nuhn M." }, { "name": "Parker A." }, { "name": "Patricio M." }, { "name": "Pignatelli M." }, { "name": "Rahtz M." }, { "name": "Riat H.S." }, { "name": "Sheppard D." }, { "name": "Taylor K." }, { "name": "Thormann A." }, { "name": "Vullo A." }, { "name": "Wilder S.P." }, { "name": "Zadissa A." }, { "name": "Birney E." }, { "name": "Harrow J." }, { "name": "Muffato M." }, { "name": "Perry E." }, { "name": "Ruffier M." }, { "name": "Spudich G." }, { "name": "Trevanion S.J." }, { "name": "Cunningham F." }, { "name": "Aken B.L." }, { "name": "Zerbino D.R." }, { "name": "Flicek P." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "Ensembl Genomes team", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "EMBL-EBI", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": null, "email": "helpdesk@ensemblgenomes.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Ensembl Genomes webteam", "email": "eg-webteam@ebi.ac.uk", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "EMBL-EBI", "additionDate": "2015-01-29T15:47:48Z", "lastUpdate": "2024-11-25T14:21:50.727694Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Ensembl Genomes Plants sequence search", "description": "Search Ensembl Plants sequences with Exonerate.", "homepage": "http://plants.ensembl.org/Multi/enasearch", "biotoolsID": "ensembl_genomes_plants_sequence_search", "biotoolsCURIE": "biotools:ensembl_genomes_plants_sequence_search", "version": [ "1" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0346", "term": "Sequence similarity search" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2044", "term": "Sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_0857", "term": "Sequence search results" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [ "Ensembl Tools", "Ensembl Genomes", "EBI Tools" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "http://www.ebi.ac.uk/about/terms-of-use", "type": [ "Terms of use" ], "note": null }, { "url": "http://plants.ensembl.org/info/website/help/index.html", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gkv1157", "pmid": "26687719", "pmcid": "PMC4702834", "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "Ensembl 2016", "abstract": "The Ensembl project (http://www.ensembl.org) is a system for genome annotation, analysis, storage and dissemination designed to facilitate the access of genomic annotation from chordates and key model organisms. It provides access to data from 87 species across our main and early access Pre! websites. This year we introduced three newly annotated species and released numerous updates across our supported species with a concentration on data for the latest genome assemblies of human, mouse, zebrafish and rat. We also provided two data updates for the previous human assembly, GRCh37, through a dedicated website (http://grch37.ensembl.org) Our tools, in particular the VEP, have been improved significantly through integration of additional third party data. REST is now capable of larger-scale analysis and our regulatory data BioMart can deliver faster results. The website is now capable of displaying long-range interactions such as those found in cis-regulated datasets. Finally we have launched a website optimized for mobile devices providing views of genes, variants and phenotypes. Our data is made available without restriction and all code is available from our GitHub organization site (http://github.com/Ensembl) under an Apache 2.0 license.", "date": "2016-01-01T00:00:00Z", "citationCount": 1097, "authors": [ { "name": "Yates A." }, { "name": "Akanni W." }, { "name": "Amode M.R." }, { "name": "Barrell D." }, { "name": "Billis K." }, { "name": "Carvalho-Silva D." }, { "name": "Cummins C." }, { "name": "Clapham P." }, { "name": "Fitzgerald S." }, { "name": "Gil L." }, { "name": "Giron C.G." }, { "name": "Gordon L." }, { "name": "Hourlier T." }, { "name": "Hunt S.E." }, { "name": "Janacek S.H." }, { "name": "Johnson N." }, { "name": "Juettemann T." }, { "name": "Keenan S." }, { "name": "Lavidas I." }, { "name": "Martin F.J." }, { "name": "Maurel T." }, { "name": "McLaren W." }, { "name": "Murphy D.N." }, { "name": "Nag R." }, { "name": "Nuhn M." }, { "name": "Parker A." }, { "name": "Patricio M." }, { "name": "Pignatelli M." }, { "name": "Rahtz M." }, { "name": "Riat H.S." }, { "name": "Sheppard D." }, { "name": "Taylor K." }, { "name": "Thormann A." }, { "name": "Vullo A." }, { "name": "Wilder S.P." }, { "name": "Zadissa A." }, { "name": "Birney E." }, { "name": "Harrow J." }, { "name": "Muffato M." }, { "name": "Perry E." }, { "name": "Ruffier M." }, { "name": "Spudich G." }, { "name": "Trevanion S.J." }, { "name": "Cunningham F." }, { "name": "Aken B.L." }, { "name": "Zerbino D.R." }, { "name": "Flicek P." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "Ensembl Genomes team", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "EMBL-EBI", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": null, "email": "helpdesk@ensemblgenomes.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Ensembl Genomes webteam", "email": "eg-webteam@ebi.ac.uk", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "EMBL-EBI", "additionDate": "2015-01-29T15:48:00Z", "lastUpdate": "2024-11-25T14:21:49.341440Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Ensembl Genomes Bacteria sequence search", "description": "Searches Ensembl Bacteria sequences using Exonerate.", "homepage": "http://bacteria.ensembl.org/Multi/enasearch", "biotoolsID": "ensembl_genomes_bacteria_sequence_search", "biotoolsCURIE": "biotools:ensembl_genomes_bacteria_sequence_search", "version": [ "1" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0346", "term": "Sequence similarity search" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2044", "term": "Sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_0857", "term": "Sequence search results" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [ "Ensembl Tools", "Ensembl Genomes", "EBI Tools" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "http://www.ebi.ac.uk/about/terms-of-use", "type": [ "Terms of use" ], "note": null }, { "url": "http://bacteria.ensembl.org/info/website/help/index.html", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gkv1157", "pmid": "26687719", "pmcid": "PMC4702834", "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "Ensembl 2016", "abstract": "The Ensembl project (http://www.ensembl.org) is a system for genome annotation, analysis, storage and dissemination designed to facilitate the access of genomic annotation from chordates and key model organisms. It provides access to data from 87 species across our main and early access Pre! websites. This year we introduced three newly annotated species and released numerous updates across our supported species with a concentration on data for the latest genome assemblies of human, mouse, zebrafish and rat. We also provided two data updates for the previous human assembly, GRCh37, through a dedicated website (http://grch37.ensembl.org) Our tools, in particular the VEP, have been improved significantly through integration of additional third party data. REST is now capable of larger-scale analysis and our regulatory data BioMart can deliver faster results. The website is now capable of displaying long-range interactions such as those found in cis-regulated datasets. Finally we have launched a website optimized for mobile devices providing views of genes, variants and phenotypes. Our data is made available without restriction and all code is available from our GitHub organization site (http://github.com/Ensembl) under an Apache 2.0 license.", "date": "2016-01-01T00:00:00Z", "citationCount": 1097, "authors": [ { "name": "Yates A." }, { "name": "Akanni W." }, { "name": "Amode M.R." }, { "name": "Barrell D." }, { "name": "Billis K." }, { "name": "Carvalho-Silva D." }, { "name": "Cummins C." }, { "name": "Clapham P." }, { "name": "Fitzgerald S." }, { "name": "Gil L." }, { "name": "Giron C.G." }, { "name": "Gordon L." }, { "name": "Hourlier T." }, { "name": "Hunt S.E." }, { "name": "Janacek S.H." }, { "name": "Johnson N." }, { "name": "Juettemann T." }, { "name": "Keenan S." }, { "name": "Lavidas I." }, { "name": "Martin F.J." }, { "name": "Maurel T." }, { "name": "McLaren W." }, { "name": "Murphy D.N." }, { "name": "Nag R." }, { "name": "Nuhn M." }, { "name": "Parker A." }, { "name": "Patricio M." }, { "name": "Pignatelli M." }, { "name": "Rahtz M." }, { "name": "Riat H.S." }, { "name": "Sheppard D." }, { "name": "Taylor K." }, { "name": "Thormann A." }, { "name": "Vullo A." }, { "name": "Wilder S.P." }, { "name": "Zadissa A." }, { "name": "Birney E." }, { "name": "Harrow J." }, { "name": "Muffato M." }, { "name": "Perry E." }, { "name": "Ruffier M." }, { "name": "Spudich G." }, { "name": "Trevanion S.J." }, { "name": "Cunningham F." }, { "name": "Aken B.L." }, { "name": "Zerbino D.R." }, { "name": "Flicek P." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "Ensembl Genomes team", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "EMBL-EBI", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": null, "email": "helpdesk@ensemblgenomes.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Ensembl Genomes webteam", "email": "eg-webteam@ebi.ac.uk", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "EMBL-EBI", "additionDate": "2015-01-29T15:48:01Z", "lastUpdate": "2024-11-25T14:21:40.171090Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "ProDom protein domain database", "description": "A comprehensive set of protein domain families automatically generated from the UniProt Knowledge Database.", "homepage": "http://prodom.prabi.fr/prodom/current/html/home.php", "biotoolsID": "prodom", "biotoolsCURIE": "biotools:prodom", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0224", "term": "Query and retrieval" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1142", "term": "ProDom accession number" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0907", "term": "Protein family report" }, "format": [ { "uri": "http://edamontology.org/format_2331", "term": "HTML" } ] } ], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0224", "term": "Query and retrieval" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1142", "term": "ProDom accession number" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1384", "term": "Sequence alignment (protein)" }, "format": [ { "uri": "http://edamontology.org/format_2331", "term": "HTML" } ] } ], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0224", "term": "Query and retrieval" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1142", "term": "ProDom accession number" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0872", "term": "Phylogenetic tree" }, "format": [ { "uri": "http://edamontology.org/format_2331", "term": "HTML" } ] } ], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0224", "term": "Query and retrieval" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1142", "term": "ProDom accession number" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1276", "term": "Nucleic acid features" }, "format": [ { "uri": "http://edamontology.org/format_2331", "term": "HTML" } ] } ], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0224", "term": "Query and retrieval" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1142", "term": "ProDom accession number" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1384", "term": "Sequence alignment (protein)" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_0623", "term": "Gene and protein families" }, { "uri": "http://edamontology.org/topic_0736", "term": "Protein folds and structural domains" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [ "DRCAT" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [ "Data" ], "elixirNode": [ "France" ], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "http://prodom.prabi.fr/prodom/current/documentation/help.php", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/28.1.267", "pmid": "10592243", "pmcid": "PMC102458", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "ProDom and ProDom-CG: Tools for protein domain analysis and whole genome comparisons", "abstract": "ProDom contains all protein domain families automatically generated from the SWISS-PROT and TrEMBL sequence databases (http://www.toulouse.inra.fr/prodom.html) ProDom-CG results from a similar domain analysis as applied to completed genomes (http://www.toulouse.inra.fr/prodomCG.html) Recent improvements to the ProDom database and its server include: scaling up to include sequences from TrEMBL, addition of Pfam-A entries to the set of expert validated families, assignment of stable accession numbers, consistency indicators for domain families, domain arrangements of sub-families and links to Pfam-A.", "date": "2000-01-01T00:00:00Z", "citationCount": 305, "authors": [ { "name": "Corpet F." }, { "name": "Servant F." }, { "name": "Gouzy J." }, { "name": "Kahn D." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "DRCAT", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Project", "typeRole": [ "Documentor" ], "note": null }, { "name": null, "email": null, "url": "http://prodom.prabi.fr/prodom/current/html/prodom_team.php", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "DRCAT", "additionDate": "2015-10-07T19:12:17Z", "lastUpdate": "2024-11-25T14:21:05.113834Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "antgenomes.org", "description": "Community database centralizing genomic and transcriptomic sequence information for ants and related species (e.g., bees and wasps). Provides BLAST search and data download. Updated periodically with latest data and new tools.", "homepage": "http://antgenomes.org", "biotoolsID": "antgenomes.org", "biotoolsCURIE": "biotools:antgenomes.org", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2421", "term": "Database search" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2044", "term": "Sequence" }, "format": [ { "uri": "http://edamontology.org/format_2200", "term": "FASTA-like (text)" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0867", "term": "Sequence alignment report" }, "format": [ { "uri": "http://edamontology.org/format_2331", "term": "HTML" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" }, { "uri": "http://edamontology.org/topic_3308", "term": "Transcriptomics" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [ "WurmLab" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "http://antgenomes.org/", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1186/1471-2164-10-5", "pmid": "19126223", "pmcid": "PMC2639375", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Fourmidable: A database for ant genomics", "abstract": "Background: Fourmidable is an infrastructure to curate and share the emerging genetic, molecular, and functional genomic data and protocols for ants. Description: The Fourmidable assembly pipeline groups nucleotide sequences into clusters before independently assembling each cluster. Subsequently, assembled sequences are annotated via Interproscan and BLAST against general and insect-specific databases. Gene-specific information can be retrieved using gene identifiers, searching for similar sequences or browsing through inferred Gene Ontology annotations. The database will readily scale as ultra-high throughput sequence data and sequences from additional species become available. Conclusion: Fourmidable currently houses EST data from two ant species and microarray gene expression data for one of these. Fourmidable is publicly available at http://fourmidable.unil.ch. © 2009 Wurm et al; licensee BioMed Central Ltd.", "date": "2009-01-06T00:00:00Z", "citationCount": 38, "authors": [ { "name": "Wurm Y." }, { "name": "Uva P." }, { "name": "Ricci F." }, { "name": "Wang J." }, { "name": "Jemielity S." }, { "name": "Iseli C." }, { "name": "Falquet L." }, { "name": "Keller L." } ], "journal": "BMC Genomics" } } ], "credit": [ { "name": "WurmLab", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Division", "typeRole": [ "Developer" ], "note": null }, { "name": "Yannick Wurm", "email": "y.wurm@qmul.ac.uk", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "bmpvieira", "additionDate": "2017-05-25T17:29:26Z", "lastUpdate": "2024-11-25T14:19:07.736913Z", "editPermission": { "type": "group", "authors": [ "priyam" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "ClustalO WS (jabaws)", "description": "JABAWS stands for JAva Bioinformatics Analysis Web Services. It is a collection of web services for bioinformatics, and currently provides services that make it easy to access well-known multiple sequence alignment and protein disorder prediction programs from Jalview.", "homepage": "http://www.compbio.dundee.ac.uk/jabaws", "biotoolsID": "clustalo_ws_jabaws", "biotoolsCURIE": "biotools:clustalo_ws_jabaws", "version": [ "1" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0492", "term": "Multiple sequence alignment" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2044", "term": "Sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Web service" ], "topic": [ { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Java" ], "license": null, "collectionID": [ "clustal", "JABAWS" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://www.biocatalogue.org/services/3687", "type": [ "Software catalogue" ], "note": null } ], "download": [], "documentation": [ { "url": "http://www.compbio.dundee.ac.uk/jabaws/man_about.html", "type": [ "User manual" ], "note": null }, { "url": "http://www.compbio.dundee.ac.uk/jabaws/full_javadoc/compbio/ws/server/ClustalOWS.html", "type": [ "API documentation" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btr304", "pmid": "21593132", "pmcid": "PMC3129525", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Java bioinformatics analysis web services for multiple sequence alignment-JABAWS:MSA", "abstract": "Summary: JABAWS is a web services framework that simplifies the deployment of web services for bioinformatics. JABAWS:MSA provides services for five multiple sequence alignment (MSA) methods (Probcons, T-coffee, Muscle, Mafft and ClustalW), and is the system employed by the Jalview multiple sequence analysis workbench since version 2.6. A fully functional, easy to set up server is provided as a Virtual Appliance (VA), which can be run on most operating systems that support a virtualization environment such as VMware or Oracle VirtualBox. JABAWS is also distributed as a Web Application aRchive (WAR) and can be configured to run on a single computer and/or a cluster managed by Grid Engine, LSF or other queuing systems that support DRMAA. JABAWS:MSA provides clients full access to each application's parameters, allows administrators to specify named parameter preset combinations and execution limits for each application through simple configuration files. The JABAWS command-line client allows integration of JABAWS services into conventional scripts. © The Author(s) 2011. Published by Oxford University Press.", "date": "2011-07-01T00:00:00Z", "citationCount": 96, "authors": [ { "name": "Troshin P.V." }, { "name": "Procter J.B." }, { "name": "Barton G.J." } ], "journal": "Bioinformatics" } } ], "credit": [ { "name": "BioCatalogue", "email": null, "url": "https://www.biocatalogue.org", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Project", "typeRole": [ "Documentor" ], "note": null }, { "name": null, "email": null, "url": "http://www.compbio.dundee.ac.uk/jabaws/contacts.html", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "BioCatalogue", "additionDate": "2015-08-03T09:36:06Z", "lastUpdate": "2024-11-25T14:17:59.498371Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null } ] }
