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assembled genomes against a user-defined marker panel.", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3196", "term": "Genotyping" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2044", "term": "Sequence" }, "format": [ { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0920", "term": "Genotype/phenotype report" }, "format": [ { "uri": "http://edamontology.org/format_3475", "term": "TSV" } ] } ], "note": "split-fastq — Alignment-free genotyping directly from raw reads using k-mer matching.", "cmd": null }, { "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_1930", "term": "FASTQ" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0920", "term": "Genotype/phenotype report" }, "format": [ { "uri": "http://edamontology.org/format_3475", "term": "TSV" } ] } ], "note": "match — Find the closest reference genome from a set of references for raw reads.", "cmd": null } ], "toolType": [ "Command-line tool", "Desktop application" ], "topic": [ { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" }, { "uri": "http://edamontology.org/topic_3301", "term": "Microbiology" }, { "uri": "http://edamontology.org/topic_0625", "term": "Genotype and phenotype" }, { "uri": "http://edamontology.org/topic_3168", "term": "Sequencing" }, { "uri": "http://edamontology.org/topic_3305", "term": "Public health and epidemiology" }, { "uri": "http://edamontology.org/topic_3474", "term": "Machine learning" } ], "operatingSystem": [], "language": [ "Rust" ], "license": "AGPL-3.0", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "https://github.com/PathoGenOmics-Lab/pathotypr/releases", "type": "Binaries", "note": null, "version": null }, { "url": "https://github.com/PathoGenOmics-Lab/pathotypr", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://github.com/PathoGenOmics-Lab/pathotypr/tree/main/docs", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.64898/2026.03.24.714002", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Paula Ruiz-Rodriguez", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0003-0727-5974", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer", "Maintainer" ], "note": null }, { "name": "Mireia Coscolla", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0003-0752-0538", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "I2SysBio (CSIC - Universitat de València)", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "PathoGenOmics Lab", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Division", "typeRole": [ "Provider" ], "note": null } ], "owner": "paururo", "additionDate": "2026-04-02T11:29:54.022786Z", "lastUpdate": "2026-04-02T11:29:54.029869Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "MHCcluster", "description": "Functional cluster of MHC class I molecules (MHCI) based on their predicted binding specificity.", "homepage": "http://cbs.dtu.dk/services/MHCcluster/", "biotoolsID": "mhccluster", "biotoolsCURIE": "biotools:mhccluster", "version": [ "2.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3459", "term": "Functional clustering" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1353", "term": "Sequence motif" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0872", "term": "Phylogenetic tree" }, "format": [ { "uri": "http://edamontology.org/format_2006", "term": "Phylogenetic tree format" } ] }, { "data": { "uri": "http://edamontology.org/data_1636", "term": "Heat map" }, "format": [ { "uri": "http://edamontology.org/format_2333", "term": "Binary format" } ] } ], "note": "provides heat-map and graphical tree-based visualizations of the functional relationship between MHC class I and class II variants", "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_2830", "term": "Immunoproteins, genes and antigens" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": "Other", "collectionID": [], "maturity": "Emerging", "cost": "Free of charge (with restrictions)", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "http://cbs.dtu.dk/services", "type": [ "Software catalogue" ], "note": null } ], "download": [], "documentation": [ { "url": "http://www.cbs.dtu.dk/services/MHCcluster-2.0/instructions.php", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1007/s00251-013-0714-9", "pmid": "23775223", "pmcid": "PMC3750724", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "MHCcluster, a method for functional clustering of MHC molecules", "abstract": "The identification of peptides binding to major histocompatibility complexes (MHC) is a critical step in the understanding of T cell immune responses. The human MHC genomic region (HLA) is extremely polymorphic comprising several thousand alleles, many encoding a distinct molecule. The potentially unique specificities remain experimentally uncharacterized for the vast majority of HLA molecules. Likewise, for nonhuman species, only a minor fraction of the known MHC molecules have been characterized. Here, we describe a tool, MHCcluster, to functionally cluster MHC molecules based on their predicted binding specificity. The method has a flexible web interface that allows the user to include any MHC of interest in the analysis. The output consists of a static heat map and graphical tree-based visualizations of the functional relationship between MHC variants and a dynamic TreeViewer interface where both the functional relationship and the individual binding specificities of MHC molecules are visualized. We demonstrate that conventional sequence-based clustering will fail to identify the functional relationship between molecules, when applied to MHC system, and only through the use of the predicted binding specificity can a correct clustering be found. Clustering of prevalent HLA-A and HLA-B alleles using MHCcluster confirms the presence of 12 major specificity groups (supertypes) some however with highly divergent specificities. Importantly, some HLA molecules are shown not to fit any supertype classification. Also, we use MHCcluster to show that chimpanzee MHC class I molecules have a reduced functional diversity compared to that of HLA class I molecules. MHCcluster is available at www.cbs.dtu.dk/services/MHCcluster-2.0. © 2013 Springer-Verlag Berlin Heidelberg.", "date": "2013-09-01T00:00:00Z", "citationCount": 60, "authors": [ { "name": "Thomsen M." }, { "name": "Lundegaard C." }, { "name": "Buus S." }, { "name": "Lund O." }, { "name": "Nielsen M." } ], "journal": "Immunogenetics" } } ], "credit": [ { "name": "CBS", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Morten Nielsen", "email": "mniel@cbs.dtu.dk", "url": null, "orcidid": "http://orcid.org/0000-0001-7885-4311", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "liuyang", "additionDate": "2015-01-21T13:29:32Z", "lastUpdate": "2026-03-20T11:08:19.028012Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "HTSlib", "description": "The main purpose of HTSlib is to provide access to genomic information files, both alignment data (SAM, BAM, and CRAM formats) and variant data (VCF and BCF formats). The library also provides interfaces to access and index genome reference data in FASTA format and tab-delimited files with genomic coordinates. It is utilized and incorporated into both SAMtools and BCFtools.", "homepage": "http://www.htslib.org/", "biotoolsID": "htslib", "biotoolsCURIE": "biotools:htslib", "version": [ "1.0", "1.1", "1.2", "1.2.1", "1.3", "1.3.1", "1.3.2", "1.4", "1.4.1", "1.5", "1.6", "1.7", "1.8", "1.9", "1.10", "1.10.1", "1.10.2", "1.11", "1.12", "1.13", "1.14", "1.15", "1.15.1", "1.16", "1.17", "1.18", "1.19", "1.20", "1.21.1", "1.22", "1.22.1", "1.22.2", "1.23", "1.23.1" ], "otherID": [], "relation": [ { "biotoolsID": "samtools", "type": "usedBy" }, { "biotoolsID": "bcftools", "type": "usedBy" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2409", "term": "Data handling" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0924", "term": "Sequence trace" }, "format": [ { "uri": "http://edamontology.org/format_3462", "term": "CRAM" }, { "uri": "http://edamontology.org/format_1929", "term": "FASTA" }, { "uri": "http://edamontology.org/format_2573", "term": "SAM" }, { "uri": "http://edamontology.org/format_2572", "term": "BAM" }, { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" } ] }, { "data": { "uri": "http://edamontology.org/data_3498", "term": "Sequence variations" }, "format": [ { "uri": "http://edamontology.org/format_3020", "term": "BCF" }, { "uri": "http://edamontology.org/format_3016", "term": "VCF" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0924", "term": "Sequence trace" }, "format": [ { "uri": "http://edamontology.org/format_3462", "term": "CRAM" }, { "uri": "http://edamontology.org/format_1929", "term": "FASTA" }, { "uri": "http://edamontology.org/format_2573", "term": "SAM" }, { "uri": "http://edamontology.org/format_2572", "term": "BAM" }, { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" } ] }, { "data": { "uri": "http://edamontology.org/data_3498", "term": "Sequence variations" }, "format": [ { "uri": "http://edamontology.org/format_3020", "term": "BCF" }, { "uri": "http://edamontology.org/format_3016", "term": "VCF" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_3071", "term": "Data management" } ], "operatingSystem": [ "Windows", "Linux", "Mac" ], "language": [ "C" ], "license": "MIT", "collectionID": [ "Animal and Crop Genomics" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/samtools/htslib", "type": [ "Repository" ], "note": null }, { "url": "http://www.htslib.org/support/#lists", "type": [ "Mailing list" ], "note": null }, { "url": "https://github.com/samtools/htslib/issues", "type": [ "Issue tracker" ], "note": null } ], "download": [ { "url": "http://www.htslib.org/download/", "type": "Downloads page", "note": null, "version": null } ], "documentation": [ { "url": "http://www.htslib.org/doc/#manual-pages", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1093/gigascience/giab007", "pmid": "33594436", "pmcid": "PMC7931820", "type": [ "Primary" ], "version": null, "note": "HTSlib: C library for reading/writing high-throughput sequencing data.", "metadata": null } ], "credit": [ { "name": "Wellcome Sanger Institute", "email": "samtools@sanger.ac.uk", "url": "https://www.sanger.ac.uk/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider", "Primary contact" ], "note": null }, { "name": "Samtools Help mailing list", "email": null, "url": "https://lists.sourceforge.net/lists/listinfo/samtools-help", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Project", "typeRole": [ "Support" ], "note": null } ], "owner": "awhitwham", "additionDate": "2017-08-20T16:07:58Z", "lastUpdate": "2026-03-18T17:33:38.200309Z", "editPermission": { "type": "group", "authors": [ "animalandcropgenomics", "smoe" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "QUAST", "description": "QUAST stands for QUality ASsessment Tool. \nIt evaluates a quality of genome assemblies by computing various metrics and providing nice reports.", "homepage": "http://quast.sourceforge.net/quast", "biotoolsID": "quast", "biotoolsCURIE": "biotools:quast", "version": [ "v.5.3.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0337", "term": "Visualisation" }, { "uri": "http://edamontology.org/operation_3180", "term": "Sequence assembly validation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1234", "term": "Sequence set (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [], "note": "# Running quast on a eukaryotic genome", "cmd": "quast -ek assembly.fa --out output_prefix" } ], "toolType": [ "Workflow" ], "topic": [ { "uri": "http://edamontology.org/topic_0196", "term": "Sequence assembly" } ], "operatingSystem": [ "Linux", "Mac" ], "language": [ "Perl", "Python", "C" ], "license": "GPL-2.0", "collectionID": [ "ONTeater" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/ablab/quast", "type": [ "Repository" ], "note": null }, { "url": "https://github.com/ablab/quast/issues", "type": [ "Issue tracker" ], "note": null } ], "download": [], "documentation": [ { "url": "http://quast.bioinf.spbau.ru/", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btt086", "pmid": "23422339", "pmcid": "PMC3624806", "type": [], "version": null, "note": null, "metadata": { "title": "QUAST: Quality assessment tool for genome assemblies", "abstract": "Limitations of genome sequencing techniques have led to dozens of assembly algorithms, none of which is perfect. A number of methods for comparing assemblers have been developed, but none is yet a recognized benchmark. Further, most existing methods for comparing assemblies are only applicable to new assemblies of finished genomes; the problem of evaluating assemblies of previously unsequenced species has not been adequately considered. Here, we present QUAST - a quality assessment tool for evaluating and comparing genome assemblies. This tool improves on leading assembly comparison software with new ideas and quality metrics. QUAST can evaluate assemblies both with a reference genome, as well as without a reference. QUAST produces many reports, summary tables and plots to help scientists in their research and in their publications. In this study, we used QUAST to compare several genome assemblers on three datasets. QUAST tables and plots for all of them are available in the Supplementary Material, and interactive versions of these reports are on the QUAST website. © 2013 The Author.", "date": "2013-04-15T00:00:00Z", "citationCount": 6872, "authors": [ { "name": "Gurevich A." }, { "name": "Saveliev V." }, { "name": "Vyahhi N." }, { "name": "Tesler G." } ], "journal": "Bioinformatics" } } ], "credit": [ { "name": "QUAST Support", "email": "quast.support@cab.spbu.ru", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "seqwiki_import", "additionDate": "2017-01-13T13:16:01Z", "lastUpdate": "2026-03-13T09:39:06.494933Z", "editPermission": { "type": "group", "authors": [ "ELIXIR-CZ", "Keiler_Collier", "rathor2611" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Mapler", "description": "Mapler is a pipeline for assessing assembly quality in taxonomically rich metagenomes sequenced with HiFi reads. It incorporates state-of-the-art metrics and facilitates the comparison of assembly strategies.", "homepage": "https://github.com/Nimauric/Mapler", "biotoolsID": "mapler", "biotoolsCURIE": "biotools:mapler", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0310", "term": "Sequence assembly" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0924", "term": "Sequence trace" }, "format": [ { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1234", "term": "Sequence set (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3180", "term": "Sequence assembly validation" }, { "uri": "http://edamontology.org/operation_3731", "term": "Sample comparison" } ], "input": [ { "data": { "uri": 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], "note": null, "cmd": null } ], "toolType": [ "Workflow", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3174", "term": "Metagenomics" }, { "uri": "http://edamontology.org/topic_0196", "term": "Sequence assembly" } ], "operatingSystem": [], "language": [ "Bash", "Python" ], "license": "AGPL-3.0", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/Nimauric/Mapler", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1093/BIOINFORMATICS/BTAF334", "pmid": "40478660", "pmcid": "PMC12205171", "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Nicolas Maurice", "email": "nicolas.maurice@inria.fr", "url": null, "orcidid": "https://orcid.org/0009-0009-9615-2765", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Claire Lemaitre", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0001-8675-170X", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Riccardo Vicedomini", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0002-7706-0998", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Clémence Frioux", "email": "clemence.frioux@inria.fr", "url": null, "orcidid": "https://orcid.org/0000-0003-2114-0697", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "owner": "nimauric", "additionDate": "2026-02-22T14:20:37.167505Z", "lastUpdate": "2026-03-10T15:44:03.311515Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "NetPhos", "description": "Neural network predictions for serine, threonine and tyrosine phosphorylation sites in eukaryotic proteins.", "homepage": "http://cbs.dtu.dk/services/NetPhos/", "biotoolsID": "netphos", "biotoolsCURIE": "biotools:netphos", "version": [ "2.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3092", "term": "Protein 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_1277", "term": "Protein features" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] }, { "data": { "uri": "http://edamontology.org/data_2955", "term": "Sequence report" }, "format": [ { "uri": "http://edamontology.org/format_2333", "term": "Binary format" } ] } ], "note": "produces neural network predictions for serine, threonine and tyrosine phosphorylation sites in eukaryotic proteins", "cmd": null } ], "toolType": [ "Command-line tool", "Web application", "Web service" ], "topic": [ { "uri": "http://edamontology.org/topic_0160", "term": "Sequence sites, features and motifs" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": "Other", "collectionID": [], "maturity": "Emerging", "cost": "Free of charge (with restrictions)", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "http://cbs.dtu.dk/services", "type": [ "Software catalogue" ], "note": null } ], "download": [], "documentation": [ { "url": "http://www.cbs.dtu.dk/services/NetPhos/instructions.php", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1006/jmbi.1999.3310", "pmid": "10600390", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Sequence and structure-based prediction of eukaryotic protein phosphorylation sites", "abstract": "Protein phosphorylation at serine, threonine or tyrosine residues affects a multitude of cellular signaling processes. How is specificity in substrate recognition and phosphorylation by protein kinases achieved? Here, we present an artificial neural network method that predicts phosphorylation sites in independent sequences with a sensitivity in the range from 69% to 96%. As an example, we predict novel phosphorylation sites in the p300/CBP protein that may regulate interaction with transcription factors and histone acetyltransferase activity. In addition, serine and threonine residues in p300/CBP that can be modified by O-linked glycosylation with N-acetylglucosamine are identified. Glycosylation may prevent phosphorplation at these sites, a mechanism named yin-yang regulation. The prediction server is available on the Internet at http://www.cbs.dtu.dk/services/NetPhos/or via e-mail to NetPhos@@@cbs.dtu.dk.", "date": "1999-12-17T00:00:00Z", "citationCount": 2373, "authors": [ { "name": "Blom N." }, { "name": "Gammeltoft S." }, { "name": "Brunak S." } ], "journal": "Journal of Molecular Biology" } } ], "credit": [ { "name": "CBS", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": null, "email": null, "url": "http://www.bioinformatics.dtu.dk/english/Service/Contact", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Nicolaj Blom", "email": "nblom@kt.dtu.dk", "url": null, "orcidid": "http://orcid.org/0000-0001-7787-7853", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "CBS", "additionDate": "2015-06-29T10:13:32Z", "lastUpdate": "2026-03-05T12:16:41.386128Z", "editPermission": { "type": "group", "authors": [ "I3raf", "Rubika" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "BigSeqKit", "description": "The Next Generation Sequencing (NGS) raw data are stored in FASTA and FASTQ text-based file formats. Common operations on FASTA/Q files include searching, filtering, sampling, deduplication and sorting, among others. We can find several tools in the literature for FASTA/Q file manipulation but none of them are well fitted for large files of tens of GB (likely TBs in the near future) since mostly they are based on sequential processing. The exception is seqkit that allows some routines to use a few threads but, in any case, the scalability is very limited. To deal with this issue, we introduce BigSeqKit, a parallel toolkit to manipulate FASTA/Q files at scale with speed and scalability at its core. BigSeqKit takes advantage of an HPC-Big Data framework (IgnisHPC) to parallelize and optimize the commands included in seqkit. In this way, in most cases it is from tens to hundreds of times faster than other state-of-the-art tools such as seqkit, samtools and pyfastx.", "homepage": "https://github.com/citiususc/BigSeqKit", "biotoolsID": "bigseqkit", "biotoolsCURIE": "biotools:bigseqkit", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3192", "term": "Sequence trimming" }, { "uri": "http://edamontology.org/operation_0372", "term": "DNA transcription" }, { "uri": "http://edamontology.org/operation_0371", "term": "DNA translation" }, { "uri": "http://edamontology.org/operation_0233", "term": "Sequence conversion" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3494", "term": "DNA sequence" }, "format": [ { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" }, { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3494", "term": "DNA sequence" }, "format": [ { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" }, { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Library", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" } ], "operatingSystem": [ "Linux" ], "language": [ "Python" ], "license": "GPL-3.0", "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "owner": "cesarpomar", "additionDate": "2023-05-22T15:10:32.141196Z", "lastUpdate": "2026-03-01T11:28:15.208151Z", "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": "cuffcompare", "description": "Compare assembled transcripts to a reference annotation and track Cufflinks transcripts across multiple experiments.", "homepage": "http://cole-trapnell-lab.github.io/cufflinks/", "biotoolsID": "cuffcompare", "biotoolsCURIE": "biotools:cuffcompare", "version": [ "2.2.1.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0492", "term": "Multiple sequence alignment" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "format": [ { "uri": "http://edamontology.org/format_1975", "term": "GFF3" }, { "uri": "http://edamontology.org/format_2306", "term": "GTF" } ] }, { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "format": [ { "uri": "http://edamontology.org/format_3475", "term": "TSV" } ] }, { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "format": [ { "uri": "http://edamontology.org/format_2306", "term": "GTF" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_3168", "term": "Sequencing" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "C++" ], "license": null, "collectionID": [ "Cufflinks", "galaxyPasteur" ], "maturity": "Mature", "cost": null, "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/fmareuil/cuffcompare/cuffcompare/2.2.1.0", "type": [ "Galaxy service" ], "note": null } ], "download": [], "documentation": [ { "url": "http://cole-trapnell-lab.github.io/cufflinks/cuffcompare/", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1038/nbt.1621", "pmid": "20436464", "pmcid": "PMC3146043", "type": [ "Primary" ], "version": null, "note": null, "metadata": null }, { "doi": "10.1093/nar/gkw343", "pmid": "27137889", "pmcid": "PMC4987906", "type": [ "Other" ], "version": null, "note": null, "metadata": null }, { "doi": "10.7490/f1000research.1114334.1", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Galaxy Support Team", "email": "galaxy@pasteur.fr", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "hmenager", "additionDate": "2016-12-19T14:29:34Z", "lastUpdate": "2026-02-26T11:14:58.790920Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "fur", "description": "The program fur takes as input a set of target genome sequences and a set of related genome sequences, the neighbors. 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"note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1093/nar/gkw343", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update", "abstract": "High-throughput data production technologies, particularly ‘next-generation’ DNA sequencing, have ushered in widespread and disruptive changes to biomedical research. Making sense of the large datasets produced by these technologies requires sophisticated statistical and computational methods, as well as substantial computational power. This has led to an acute crisis in life sciences, as researchers without informatics training attempt to perform computation-dependent analyses. Since 2005, the Galaxy project has worked to address this problem by providing a framework that makes advanced computational tools usable by non experts. Galaxy seeks to make data-intensive research more accessible, transparent and reproducible by providing a Web-based environment in which users can perform computational analyses and have all of the details automatically tracked for later inspection, publication, or reuse. In this report we highlight recently added features enabling biomedical analyses on a large scale.", "date": "2016-07-08T00:00:00Z", "citationCount": 1477, "authors": [ { "name": "Afgan E." }, { "name": "Baker D." }, { "name": "van den Beek M." }, { "name": "Blankenberg D." }, { "name": "Bouvier D." }, { "name": "Cech M." }, { "name": "Chilton J." }, { "name": "Clements D." }, { "name": "Coraor N." }, { "name": "Eberhard C." }, { "name": "Gruning B." }, { "name": "Guerler A." }, { "name": "Hillman-Jackson J." }, { "name": "Kuster G.V." }, { "name": "Rasche E." }, { "name": "Soranzo N." }, { "name": "Turaga N." }, { "name": "Taylor J." }, { "name": "Nekrutenko A." }, { "name": "Goecks J." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.7490/f1000research.1114334.1", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Galaxy Support Team", "email": "galaxy@pasteur.fr", "url": null, "orcidid": null, 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The availability of large-scale sequence data from various high-throughput platforms has opened possibilities to identify, predict, and functionally annotate lncRNAs. As a result, there is a growing demand for an integrative computational framework capable of identifying known lncRNAs, predicting novel lncRNAs, and inferring the downstream regulatory interactions of lncRNAs at the genome-scale. We present ETENLNC (End-To-End-Novel-Long-NonCoding), a user-friendly, integrative, open-source, scalable, and modular computational framework for identifying and analyzing lncRNAs from raw RNA-Seq data. ETENLNC employs six stringent filtration steps to identify novel lncRNAs, performs differential expression analysis of mRNA and lncRNA transcripts, and predicts regulatory interactions between lncRNAs, mRNAs, miRNAs, and proteins. We benchmarked ETENLNC against six existing tools and optimized it for desktop workstations and high-performance computing environments using data from three different species. ETENLNC is freely available on GitHub: https://github.com/EvolOMICS-TU/ETENLNC.", "date": "2024-10-01T00:00:00Z", "citationCount": 2, "authors": [ { "name": "Nath P." }, { "name": "Bhuyan K." }, { "name": "Bhattacharyya D.K." }, { "name": "Barah P." } ], "journal": "Computational Biology and Chemistry" } } ], "credit": [ { "name": "Pankaj Barah", "email": "barah@tezu.ernet.in", "url": "https://www.tezu.ernet.in/dmbbt/profile/34", "orcidid": "https://orcid.org/0000-0001-7039-7996", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Maintainer" ], "note": "Assistant Professor at Department of Molecular Biology and Biotechnology, Tezpur University." }, { "name": "Prangan Nath", "email": "prangannathofficial@gmai.com", "url": null, "orcidid": "https://orcid.org/0000-0002-9451-7822", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer", "Maintainer" ], "note": null } ], "owner": "prangannath", "additionDate": "2025-07-23T10:27:57.572501Z", "lastUpdate": "2025-07-23T10:27:57.574879Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "MirGeneDB", "description": "MirGeneDB is a database of manually curated microRNA genes that have been validated and annotated as initially described in Fromm et al. 2015 , Fromm et al. 2020 and Fromm et al 2022. MirGeneDB 3.0 (Clarke and Hoye et al. 2024 ) includes more than 21,000 microRNA gene entries representing more than 1,700 microRNA families from 114 metazoan species. 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Adhering to uniform and consistent criteria for microRNA annotation and nomenclature, we substantially expanded MirGeneDB with 30 additional species representing previously missing metazoan phyla such as sponges, jellyfish, rotifers and flatworms. MirGeneDB 2.1 now consists of 75 species spanning over ∼800 million years of animal evolution, and contains a total number of 16 670 microRNAs from 1549 families. Over 6000 microRNAs were added in this update using ∼550 datasets with ∼7.5 billion sequencing reads. By adding new phylogenetically important species, especially those relevant for the study of whole genome duplication events, and through updating evolutionary nodes of origin for many families and genes, we were able to substantially refine our nomenclature system. All changes are traceable in the specifically developed MirGeneDB version tracker. The performance of read-pages is improved and microRNA expression matrices for all tissues and species are now also downloadable. Altogether, this update represents a significant step toward a complete sampling of all major metazoan phyla, and a widely needed foundation for comparative microRNA genomics and transcriptomics studies. MirGeneDB 2.1 is part of RNAcentral and Elixir Norway, publicly and freely available at http://www.mirgenedb.org/.", "date": "2022-01-07T00:00:00Z", "citationCount": 95, "authors": [ { "name": "Fromm B." }, { "name": "Hoye E." }, { "name": "Domanska D." }, { "name": "Zhong X." }, { "name": "Aparicio-Puerta E." }, { "name": "Ovchinnikov V." }, { "name": "Umu S.U." }, { "name": "Chabot P.J." }, { "name": "Kang W." }, { "name": "Aslanzadeh M." }, { "name": "Tarbier M." }, { "name": "Marmol-Sanchez E." }, { "name": "Urgese G." }, { "name": "Johansen M." }, { "name": "Hovig E." }, { "name": "Hackenberg M." }, { "name": "Friedlander M.R." }, { "name": "Peterson K.J." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/nar/gkz885", "pmid": "31598695", "pmcid": "PMC6943042", "type": [ "Primary" ], "version": "2.0", "note": null, "metadata": { "title": "MirGeneDB 2.0: The metazoan microRNA complement", "abstract": "Small non-coding RNAs have gained substantial attention due to their roles in animal development and human disorders. Among them, microRNAs are special because individual gene sequences are conserved across the animal kingdom. In addition, unique and mechanistically well understood features can clearly distinguish bona fide miRNAs from the myriad other small RNAs generated by cells. However, making this distinction is not a common practice and, thus, not surprisingly, the heterogeneous quality of available miRNA complements has become a major concern in microRNA research. We addressed this by extensively expanding our curated microRNA gene database-MirGeneDB-to 45 organisms, encompassing a wide phylogenetic swath of animal evolution. By consistently annotating and naming 10,899 microRNA genes in these organisms, we show that previous microRNA annotations contained not only many false positives, but surprisingly lacked >2000 bona fide microRNAs. Indeed, curated microRNA complements of closely related organisms are very similar and can be used to reconstruct ancestral miRNA repertoires. MirGeneDB represents a robust platform for microRNA-based research, providing deeper and more significant insights into the biology and evolution of miRNAs as well as biomedical and biomarker research. MirGeneDB is publicly and freely available at http://mirgenedb.org/.", "date": "2020-01-01T00:00:00Z", "citationCount": 178, "authors": [ { "name": "Fromm B." }, { "name": "Domanska D." }, { "name": "Hoye E." }, { "name": "Ovchinnikov V." }, { "name": "Kang W." }, { "name": "Aparicio-Puerta E." }, { "name": "Johansen M." }, { "name": "Flatmark K." }, { "name": "Mathelier A." }, { "name": "Hovig E." }, { "name": "Hackenberg M." }, { "name": "Friedlander M.R." }, { "name": "Peterson K.J." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1146/annurev-genet-120213-092023", "pmid": "26473382", "pmcid": "PMC4743252", "type": [ "Primary" ], "version": "1.0", "note": null, "metadata": { "title": "A Uniform System for the Annotation of Vertebrate microRNA Genes and the Evolution of the Human microRNAome", "abstract": "Although microRNAs (miRNAs) are among the most intensively studied molecules of the past 20 years, determining what is and what is not a miRNA has not been straightforward. Here, we present a uniform system for the annotation and nomenclature of miRNA genes. We show that less than a third of the 1,881 human miRBase entries, and only approximately 16% of the 7,095 metazoan miRBase entries, are robustly supported as miRNA genes. Furthermore, we show that the human repertoire of miRNAs has been shaped by periods of intense miRNA innovation and that mature gene products show a very different tempo and mode of sequence evolution than star products. We establish a new open access database-MirGeneDB (http://mirgenedb.org)-to catalog this set of miRNAs, which complements the efforts of miRBase but differs from it by annotating the mature versus star products and by imposing an evolutionary hierarchy upon this curated and consistently named repertoire.", "date": "2015-11-23T00:00:00Z", "citationCount": 435, "authors": [ { "name": "Fromm B." }, { "name": "Billipp T." }, { "name": "Peck L.E." }, { "name": "Johansen M." }, { "name": "Tarver J.E." }, { "name": "King B.L." }, { "name": "Newcomb J.M." }, { "name": "Sempere L.F." }, { "name": "Flatmark K." }, { "name": "Hovig E." }, { "name": "Peterson K.J." } ], "journal": "Annual Review of Genetics" } }, { "doi": "10.1093/nar/gkae1094", "pmid": "39673268", "pmcid": "PMC11701709", "type": [ "Primary" ], "version": "3.0", "note": null, "metadata": { "title": "MirGeneDB 3.0: Improved taxonomic sampling, uniform nomenclature of novel conserved microRNA families and updated covariance models", "abstract": "We present a major update of MirGeneDB (3.0), the manually curated animal microRNA gene database. Beyond moving to a new server and the creation of a computational mirror, we have expanded the database with the addition of 33 invertebrate species, including representatives of 5 previously unsampled phyla, and 6 mammal species. MirGeneDB now contains entries for 21 822 microRNA genes (5160 of these from the new species) belonging to 1743 microRNA families. The inclusion of these new species allowed us to refine both the evolutionary node of appearance of a number of microRNA genes/families, as well as MirGeneDB's phylogenetically informed nomenclature system. Updated covariance models of all microRNA families, along with all smallRNA read data are now downloadable. These enhanced annotations will allow researchers to analyze microRNA properties such as secondary structure and features of their biogenesis within a robust phylogenetic context and without the database plagued with numerous false positives and false negatives. In light of these improvements, MirGeneDB 3.0 will assume the responsibility for naming conserved novel metazoan microRNAs. MirGeneDB is part of RNAcentral and Elixir Norway and is publicly and freely available at mirgenedb.org.", "date": "2025-01-06T00:00:00Z", "citationCount": 6, "authors": [ { "name": "Clarke A.W." }, { "name": "Hoye E." }, { "name": "Hembrom A.A." }, { "name": "Paynter V.M." }, { "name": "Vinther J." }, { "name": "Wyrozemski L." }, { "name": "Biryukova I." }, { "name": "Formaggioni A." }, { "name": "Ovchinnikov V." }, { "name": "Herlyn H." }, { "name": "Pierce A." }, { "name": "Wu C." }, { "name": "Aslanzadeh M." }, { "name": "Cheneby J." }, { "name": "Martinez P." }, { "name": "Friedlander M.R." }, { "name": "Hovig E." }, { "name": "Hackenberg M." }, { "name": "Umu S.U." }, { "name": "Johansen M." }, { "name": "Peterson K.J." }, { "name": "Fromm B." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "Bastian Fromm", "email": "BastianFromm@gmail.com", "url": null, "orcidid": "https://orcid.org/0000-0003-0352-3037", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer", "Maintainer", "Support" ], "note": null }, { "name": "Kevin J. 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Among all the steps, although step 4 is optional, we highly recommend our users to do so, because assemblers may produce overrepresented seqeuences. 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It uses the SILVA rDNA databases, taxonomies, and alignments as a reference. It facilitates the classification of rDNA reads and provides a wealth of results (tables, graphs and sequence files) for download.", "homepage": "https://ngs.arb-silva.de", "biotoolsID": "silvangs", "biotoolsCURIE": "biotools:silvangs", "version": [ "1.9.10" ], "otherID": [], "relation": [ { "biotoolsID": "silva", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0337", "term": "Visualisation" }, { "uri": "http://edamontology.org/operation_2238", "term": "Statistical calculation" }, { "uri": "http://edamontology.org/operation_2478", "term": "Nucleic acid sequence analysis" }, { "uri": "http://edamontology.org/operation_3460", "term": "Taxonomic classification" }, { "uri": "http://edamontology.org/operation_2428", "term": "Validation" }, { "uri": "http://edamontology.org/operation_0291", "term": "Sequence clustering" }, { "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" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2082", "term": "Matrix" }, "format": [ { "uri": "http://edamontology.org/format_3475", "term": "TSV" } ] }, { "data": { "uri": "http://edamontology.org/data_2884", "term": "Plot" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2048", "term": "Report" }, "format": [ { "uri": "http://edamontology.org/format_3508", "term": "PDF" } ] }, { "data": { "uri": "http://edamontology.org/data_1246", "term": "Sequence cluster (nucleic acid)" }, "format": [ { "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 pipeline accepts input data in Multi-Fasta format with each input file representing one sample. Samples that belong to one project (a transect, timeseries etc.) should be uploaded as a single SILVAngs project.", "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_3174", "term": "Metagenomics" }, { "uri": "http://edamontology.org/topic_3050", "term": "Biodiversity" }, { "uri": "http://edamontology.org/topic_0637", "term": "Taxonomy" }, { "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_3697", "term": "Microbial ecology" } ], "operatingSystem": [], "language": [], "license": null, "collectionID": [ "de.NBI", "de.NBI-biodata", "DSMZ Digital Diversity" ], "maturity": "Mature", "cost": "Free of charge (with restrictions)", "accessibility": null, "elixirPlatform": [ "Data" ], "elixirNode": [ "Germany" ], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://www.arb-silva.de/fileadmin/silva_databases/sngs/SILVAngs_User_Guide.pdf", "type": [ "User manual" ], "note": null }, { "url": "https://www.arb-silva.de/documentation/silvangs/userfaq/", "type": [ "FAQ" ], "note": null }, { "url": "https://www.arb-silva.de/footer/sngs-termsofuse", "type": [ "Terms of use" ], "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": [ "Primary" ], "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/bioinformatics/bts252", "pmid": "22556368", "pmcid": "PMC3389763", "type": [ "Primary" ], "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" } } ], "credit": [ { "name": "SILVA Team", "email": "ngs-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 }, { "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 } ], "owner": "silva", "additionDate": "2016-09-30T07:30:11Z", "lastUpdate": "2025-06-30T13:26:39.251875Z", "editPermission": { "type": "group", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "DeepSig", "description": "Prediction of secretory signal peptides in protein sequences", "homepage": "https://busca.biocomp.unibo.it/deepsig/", "biotoolsID": "deepsig", "biotoolsCURIE": "biotools:deepsig", "version": [ "1.2.5" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0418", "term": "Protein signal peptide detection" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2974", "term": "Protein sequence (raw)" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_3028", "term": "Taxonomy" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0896", "term": "Protein report" }, "format": [ { "uri": "http://edamontology.org/format_2331", "term": "HTML" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Web application", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3307", "term": "Computational biology" }, { "uri": "http://edamontology.org/topic_3510", "term": "Protein sites, features and motifs" }, { "uri": "http://edamontology.org/topic_0123", "term": "Protein properties" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Python", "C++" ], "license": "GPL-3.0", "collectionID": [ "Bologna Biocomputing Group" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [ "Italy" ], "elixirCommunity": [], "link": [], "download": [ { "url": "https://github.com/BolognaBiocomp/deepsig", "type": "Source code", "note": null, "version": "1.2.5" }, { "url": "https://hub.docker.com/r/bolognabiocomp/deepsig", "type": "Container file", "note": null, "version": "1.2.5" } ], "documentation": [ { "url": "https://github.com/BolognaBiocomp/deepsig", "type": [ "Command-line options" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btx818", "pmid": "29280997", "pmcid": "PMC5946842", "type": [ "Primary" ], "version": "1.0", "note": null, "metadata": { "title": "DeepSig: Deep learning improves signal peptide detection in proteins", "abstract": "Motivation The identification of signal peptides in protein sequences is an important step toward protein localization and function characterization. Results Here, we present DeepSig, an improved approach for signal peptide detection and cleavage-site prediction based on deep learning methods. Comparative benchmarks performed on an updated independent dataset of proteins show that DeepSig is the current best performing method, scoring better than other available state-of-the-art approaches on both signal peptide detection and precise cleavage-site identification. Availability and implementation DeepSig is available as both standalone program and web server at https://deepsig.biocomp.unibo.it. All datasets used in this study can be obtained from the same website.", "date": "2018-05-15T00:00:00Z", "citationCount": 96, "authors": [ { "name": "Savojardo C." }, { "name": "Martelli P.L." }, { "name": "Fariselli P." }, { "name": "Casadio R." } ], "journal": "Bioinformatics" } } ], "credit": [ { "name": "ELIXIR-ITA-BOLOGNA", "email": null, "url": "http://biocomp.unibo.it", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Castrense Savojardo", "email": "castrense.savojardo2@unibo.it", "url": null, "orcidid": "https://orcid.org/0000-0002-7359-0633", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer", "Primary contact" ], "note": null }, { "name": "Pier Luigi Martelli", "email": "pierluigi.martelli@unibo.it", "url": "http://biocomp.unibo.it", "orcidid": "https://orcid.org/0000-0002-0274-5669", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "ELIXIR-ITA-BOLOGNA", "additionDate": "2018-05-28T14:50:09Z", "lastUpdate": "2025-06-19T11:55:09.017105Z", "editPermission": { "type": "group", "authors": [ "savo", "ELIXIR-ITA-BOLOGNA" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" } ] }
