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{ "count": 13, "next": "?page=2", "previous": null, "list": [ { "name": "trimAl", "description": "Tool for the automated removal of spurious sequences or poorly aligned regions from a multiple sequence alignment.", "homepage": "http://trimal.cgenomics.org", "biotoolsID": "trimal", "biotoolsCURIE": "biotools:trimal", "version": [ "1.4", "2.0-RC" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0492", "term": "Multiple sequence alignment" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1916", "term": "Alignment" }, "format": [ { "uri": "http://edamontology.org/format_1982", "term": "ClustalW format" }, { "uri": "http://edamontology.org/format_1997", "term": "PHYLIP format" }, { "uri": "http://edamontology.org/format_1998", "term": "phylipnon" }, { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_2048", "term": "Report" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/topic_3168", "term": "Sequencing" }, { "uri": "http://edamontology.org/topic_0160", "term": "Sequence sites, features and motifs" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "C++" ], "license": null, "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/inab/trimal", "type": [ "Repository" ], "note": null } ], "download": [ { "url": "https://github.com/inab/trimal", "type": "Source code", "note": null, "version": "1.4" }, { "url": "https://github.com/inab/trimal/tree/2.0_RC", "type": "Source code", "note": null, "version": "2.0-RC" } ], "documentation": [ { "url": "http://trimal.cgenomics.org/", "type": [ "General" ], "note": "Version 1.2" }, { "url": "https://trimal.readthedocs.io", "type": [ "General" ], "note": "Version 1.4 and 2 (not updated)" } ], "publication": [ { "doi": null, "pmid": "19505945", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "trimAl: A tool for automated alignment trimming in large-scale phylogenetic analyses", "abstract": "Multiple sequence alignments are central to many areas of bioinformatics. It has been shown that the removal of poorly aligned regions from an alignment increases the quality of subsequent analyses. Such an alignment trimming phase is complicated in large-scale phylogenetic analyses that deal with thousands of alignments. Here, we present trimAl, a tool for automated alignment trimming, which is especially suited for large-scale phylogenetic analyses. trimAl can consider several parameters, alone or in multiple combinations, for selecting the most reliable positions in the alignment. These include the proportion of sequences with a gap, the level of amino acid similarity and, if several alignments for the same set of sequences are provided, the level of consistency across different alignments. Moreover, trimAl can automatically select the parameters to be used in each specific alignment so that the signal-to-noise ratio is optimized. © 2009 The Author(s).", "date": "2009-08-01T00:00:00Z", "citationCount": 5669, "authors": [ { "name": "Capella-Gutierrez S." }, { "name": "Silla-Martinez J.M." }, { "name": "Gabaldon T." } ], "journal": "Bioinformatics" } } ], "credit": [ { "name": "Salvador Capella-Gutierrez", "email": "salcagu@gmail.com", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": null, "email": "tgabaldon@crg.es", "url": "http://gabaldonlab.crg.es/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "community": null, "owner": "scapella", "additionDate": "2017-04-15T08:42:53Z", "lastUpdate": "2023-12-20T11:14:33.125452Z", "editPermission": { "type": "group", "authors": [ "nico_bsc", "sergitobara" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Jalview", "description": "Jalview is a free program for multiple sequence alignment editing, visualisation and analysis. Use it to 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": [ "2.11.3.2" ], "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" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0564", "term": "Sequence visualisation" }, { "uri": "http://edamontology.org/operation_0324", "term": "Phylogenetic tree analysis" }, { "uri": "http://edamontology.org/operation_3081", "term": "Sequence alignment editing" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_1939", "term": "GFF3-seq" }, { "uri": "http://edamontology.org/format_1982", "term": "ClustalW format" }, { "uri": "http://edamontology.org/format_1961", "term": "Stockholm format" }, { "uri": "http://edamontology.org/format_1984", "term": "FASTA-aln" }, { "uri": "http://edamontology.org/format_1938", "term": "GFF2-seq" }, { "uri": "http://edamontology.org/format_1929", "term": "FASTA" }, { "uri": "http://edamontology.org/format_1948", "term": "nbrf/pir" }, { "uri": "http://edamontology.org/format_3774", "term": "BioJSON (Jalview)" }, { "uri": "http://edamontology.org/format_1997", "term": "PHYLIP format" }, { "uri": "http://edamontology.org/format_3313", "term": "BLC" }, { "uri": "http://edamontology.org/format_3311", "term": "RNAML" }, { "uri": "http://edamontology.org/format_1947", "term": "GCG MSF" }, { "uri": "http://edamontology.org/format_3015", "term": "Pileup" }, { "uri": "http://edamontology.org/format_1477", "term": "mmCIF" }, { "uri": "http://edamontology.org/format_3016", "term": "VCF" }, { "uri": "http://edamontology.org/format_1915", "term": "Format" } ] }, { "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_3464", "term": "JSON" }, { "uri": "http://edamontology.org/format_1961", "term": "Stockholm format" }, { "uri": "http://edamontology.org/format_1929", "term": "FASTA" }, { "uri": "http://edamontology.org/format_1997", "term": "PHYLIP format" }, { "uri": "http://edamontology.org/format_3313", "term": "BLC" }, { "uri": "http://edamontology.org/format_3774", "term": "BioJSON (Jalview)" }, { "uri": "http://edamontology.org/format_1947", "term": "GCG MSF" }, { "uri": "http://edamontology.org/format_3015", "term": "Pileup" }, { "uri": "http://edamontology.org/format_1982", "term": "ClustalW format" } ] }, { "data": { "uri": "http://edamontology.org/data_2884", "term": "Plot" }, "format": [ { "uri": "http://edamontology.org/format_3603", "term": "PNG" }, { "uri": "http://edamontology.org/format_2331", "term": "HTML" }, { "uri": "http://edamontology.org/format_3466", "term": "EPS" }, { "uri": "http://edamontology.org/format_3604", "term": "SVG" }, { "uri": "http://edamontology.org/format_1915", "term": "Format" } ] } ], "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": [ "Linux", "Windows", "Mac" ], "language": [], "license": "GPL-3.0", "collectionID": [ "ELIXIR-UK" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [ "Tools" ], "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://source.jalview.org/crucible/browse/jalview", "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" } ], "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": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Jalview Version 2-A multiple sequence alignment editor and analysis workbench", "abstract": "Summary: Jalview Version 2 is a system for interactive WYSIWYG editing, analysis and annotation of multiple sequence alignments. Core features include keyboard and mouse-based editing, multiple views and alignment overviews, and linked structure display with Jmol. Jalview 2 is available in two forms: a lightweight Java applet for use in web applications, and a powerful desktop application that employs web services for sequence alignment, secondary structure prediction and the retrieval of alignments, sequences, annotation and structures from public databases and any DAS 1.53 compliant sequence or annotation server. © 2009 The Author(s).", "date": "2009-05-07T00:00:00Z", "citationCount": 6231, "authors": [ { "name": "Waterhouse A.M." }, { "name": "Procter J.B." }, { "name": "Martin D.M.A." }, { "name": "Clamp M." }, { "name": "Barton G.J." } ], "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 } ], "community": null, "owner": "ben_s", "additionDate": "2019-02-13T17:01:40Z", "lastUpdate": "2023-12-01T12:00:21.286261Z", "editPermission": { "type": "group", "authors": [ "ben_s", "jimprocter" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "kc-align", "description": "A fast and accurate tool for performing codon-aware multiple sequence alignments", "homepage": "https://github.com/davebx/kc-align", "biotoolsID": "kc-align", "biotoolsCURIE": "biotools:kc-align", "version": [ "1.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0492", "term": "Multiple sequence alignment" } ], "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_1383", "term": "Nucleic acid sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_1982", "term": "ClustalW format" }, { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "note": null, "cmd": "kc-align -m genome -r reference.fasta -S sequences.fasta -s 3532,3892 -e 3894,5326" } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0102", "term": "Mapping" } ], "operatingSystem": [], "language": [], "license": "AFL-3.0", "collectionID": [], "maturity": null, "cost": null, "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "community": null, "owner": "m.bernt", "additionDate": "2022-06-24T09:15:31.387295Z", "lastUpdate": "2022-06-24T09:15:31.390005Z", "editPermission": { "type": "public", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "MUSCLE", "description": "This tool performs multiple sequence alignments of nucleotide or amino acid sequences.", "homepage": "https://www.drive5.com/muscle/", "biotoolsID": "muscle", "biotoolsCURIE": "biotools:muscle", "version": [ "5" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0492", "term": "Multiple sequence alignment" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3494", "term": "DNA 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_3495", "term": "RNA 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_0863", "term": "Sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_1982", "term": "ClustalW format" }, { "uri": "http://edamontology.org/format_2331", "term": "HTML" }, { "uri": "http://edamontology.org/format_1997", "term": "PHYLIP format" }, { "uri": "http://edamontology.org/format_1947", "term": "GCG MSF" }, { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool", "Web API" ], "topic": [ { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": "Other", "collectionID": [ "MUSCLE", "galaxyPasteur", "BioConductor" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://www.biocatalogue.org/services/3135", "type": [ "Software catalogue" ], "note": null }, { "url": "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/fmareuil/oneclick_phylogeny/muscle/3.8.31.1", "type": [ "Galaxy service" ], "note": null } ], "download": [ { "url": "http://bioconductor/packages/release/bioc/src/contrib/muscle_3.16.0.tar.gz", "type": "Source code", "note": "BioConductor package", "version": null }, { "url": "https://www.ebi.ac.uk/seqdb/confluence/display/WEBSERVICES/muscle_rest", "type": "API specification", "note": "EBI MUSCLE Web Service", "version": null }, { "url": "https://www.drive5.com/muscle/downloads.htm", "type": "Downloads page", "note": null, "version": null } ], "documentation": [ { "url": "http://bioconductor.org/packages/release/bioc/html/muscle.html", "type": [ "User manual" ], "note": "BioConductor package documentation" }, { "url": "https://www.ebi.ac.uk/seqdb/confluence/display/WEBSERVICES/muscle_rest", "type": [ "API documentation" ], "note": "EBI Web Service documentation" }, { "url": "https://www.drive5.com/muscle/manual/", "type": [ "User manual" ], "note": null }, { "url": "https://www.drive5.com/muscle/manual/install.html", "type": [ "Installation instructions" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gkh340", "pmid": "15034147", "pmcid": "PMC390337", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "MUSCLE: Multiple sequence alignment with high accuracy and high throughput", "abstract": "We describe MUSCLE, a new computer program for creating multiple alignments of protein sequences. Elements of the algorithm include fast distance estimation using kmer counting, progressive alignment using a new profile function we call the log-expectation score, and refinement using tree-dependent restricted partitioning. The speed and accuracy of MUSCLE are compared with T-Coffee, MAFFT and CLUSTALW on four test sets of reference alignments: BAliBASE, SABmark, SMART and a new benchmark, PREFAB. MUSCLE achieves the highest, or joint highest, rank in accuracy on each of these sets. Without refinement, MUSCLE achieves average accuracy statistically indistinguishable from T-Coffee and MAFFT, and is the fastest of the tested methods for large numbers of sequences, aligning 5000 sequences of average length 350 in 7 min on a current desktop computer. The MUSCLE program, source code and PREFAB test data are freely available at http://www.drive5.com/muscle. © Oxford University Press 20004; all rights reserved.", "date": "2004-07-09T00:00:00Z", "citationCount": 27922, "authors": [ { "name": "Edgar R.C." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.7490/f1000research.1114334.1", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": null }, { "doi": "10.1186/1471-2105-5-113", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "MUSCLE: A multiple sequence alignment method with reduced time and space complexity", "abstract": "Background: In a previous paper, we introduced MUSCLE, a new program for creating multiple alignments of protein sequences, giving a brief summary of the algorithm and showing MUSCLE to achieve the highest scores reported to date on four alignment accuracy benchmarks. Here we present a more complete discussion of the algorithm, describing several previously unpublished techniques that improve biological accuracy and / or computational complexity. We introduce a new option, MUSCLE-fast, designed for high-throughput applications. We also describe a new protocol for evaluating objective functions that align two profiles. Results: We compare the speed and accuracy of MUSCLE with CLUSTALW, Progressive POA and the MAFFT script FFTNS1, the fastest previously published program known to the author. Accuracy is measured using four benchmarks: BAliBASE, PREFAB, SABmark and SMART. We test three variants that offer highest accuracy (MUSCLE with default settings), highest speed (MUSCLEfast), and a carefully chosen compromise between the two (MUSCLE-prog). We find MUSCLE-fast to be the fastest algorithm on all test sets, achieving average alignment accuracy similar to CLUSTALW in times that are typically two to three orders of magnitude less. MUSCLE-fast is able to align 1,000 sequences of average length 282 in 21 seconds on a current desktop computer. Conclusions: MUSCLE offers a range of options that provide improved speed and / or alignment accuracy compared with currently available programs. MUSCLE is freely available at http:// www.drive5.com/muscle. © 2004 Edgar; licensee BioMed Central Ltd.", "date": "2004-08-19T00:00:00Z", "citationCount": 5444, "authors": [ { "name": "Edgar R.C." } ], "journal": "BMC Bioinformatics" } }, { "doi": "10.1101/2021.06.20.449169", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": "5", "note": null, "metadata": null } ], "credit": [ { "name": "Alex T. Kalinka", "email": "alex.t.kalinka@gmail.com", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Maintainer" ], "note": "Maintainer of the BioConductor package" }, { "name": null, "email": null, "url": "http://www.ebi.ac.uk/support/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": "EBI Web Service support" }, { "name": "Technical Support", "email": null, "url": "https://www.drive5.com/muscle/manual/support.html", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Robert Edgar", "email": "robert@drive5.com", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer" ], "note": null } ], "community": { "biolib": { "app_name": "MUSCLE", "author_name": "bio-utils", "author_username": "bio-utils" } }, "owner": "bioconductor_import", "additionDate": "2017-01-17T14:57:39Z", "lastUpdate": "2022-04-26T14:33:24.095367Z", "editPermission": { "type": "group", "authors": [ "laurasansc" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "ClustalW (BioLib)", "description": "ClustalW is a general purpose multiple sequence alignment program for DNA or proteins", "homepage": "https://biolib.com/bio-utils/clustalw/", "biotoolsID": "clustalw_biolib", "biotoolsCURIE": "biotools:clustalw_biolib", "version": [ "2.1." ], "otherID": [], "relation": [], "function": [ { "operation": [ { "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" } ] } ], "output": [ { "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_1929", "term": "FASTA" }, { "uri": "http://edamontology.org/format_1949", "term": "nexus-seq" }, { "uri": "http://edamontology.org/format_1997", "term": "PHYLIP format" } ] } ], "note": null, "cmd": "clustalw -INPUT=sequences.fasta -OUTFILE=alignment.fasta -OUTPUT=FASTA" } ], "toolType": [ "Web application", "Web API", "Command-line tool", "Bioinformatics portal" ], "topic": [ { "uri": "http://edamontology.org/topic_3293", "term": "Phylogenetics" }, { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [], "license": "LGPL-3.0", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "http://www.clustal.org/clustal2/", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btm404", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Clustal W and Clustal X version 2.0", "abstract": "Summary: The Clustal W and Clustal X multiple sequence alignment programs have been completely rewritten in C++. This will facilitate the further development of the alignment algorithms in the future and has allowed proper porting of the programs to the latest versions of Linux, Macintosh and Windows operating systems. © The Author 2007. Published by Oxford University Press. All rights reserved.", "date": "2007-11-01T00:00:00Z", "citationCount": 20602, "authors": [ { "name": "Larkin M.A." }, { "name": "Blackshields G." }, { "name": "Brown N.P." }, { "name": "Chenna R." }, { "name": "Mcgettigan P.A." }, { "name": "McWilliam H." }, { "name": "Valentin F." }, { "name": "Wallace I.M." }, { "name": "Wilm A." }, { "name": "Lopez R." }, { "name": "Thompson J.D." }, { "name": "Gibson T.J." }, { "name": "Higgins D.G." } ], "journal": "Bioinformatics" } } ], "credit": [], "community": { "biolib": { "app_name": "clustalw", "author_name": "bio-utils", "author_username": "bio-utils" } }, "owner": "laurasansc", "additionDate": "2021-10-22T10:16:40.495992Z", "lastUpdate": "2021-10-22T10:23:07.958199Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "WAR", "description": "Easy-to-use webserver that makes it possible to simultaneously use the best methods for aligning and predicting the consensus secondary structure for a set of non-coding RNA sequences.", "homepage": "http://genome.ku.dk/resources/war/", "biotoolsID": "war", "biotoolsCURIE": "biotools:war", "version": [ "1" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0278", "term": "RNA secondary structure prediction" }, { "uri": "http://edamontology.org/operation_0292", "term": "Sequence alignment" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3495", "term": "RNA sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_1961", "term": "Stockholm format" } ] } ], "output": [ { "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_1961", "term": "Stockholm format" }, { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "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": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "http://genome.ku.dk/resources/war/pages/about.php", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gkn275", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "WAR: Webserver for aligning structural RNAs.", "abstract": "We present an easy-to-use webserver that makes it possible to simultaneously use a number of state of the art methods for performing multiple alignment and secondary structure prediction for noncoding RNA sequences. This makes it possible to use the programs without having to download the code and get the programs to run. The results of all the programs are presented on a webpage and can easily be downloaded for further analysis. Additional measures are calculated for each program to make it easier to judge the individual predictions, and a consensus prediction taking all the programs into account is also calculated. This website is free and open to all users and there is no login requirement. The webserver can be found at: http://genome.ku.dk/resources/war.", "date": "2008-01-01T00:00:00Z", "citationCount": 36, "authors": [ { "name": "Torarinsson E." }, { "name": "Lindgreen S." } ], "journal": "Nucleic acids research" } } ], "credit": [ { "name": "binf.ku.dk", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Stinus Lindgreen", "email": "stinus@binf.ku.dk", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "community": null, "owner": "admin", "additionDate": "2015-07-28T11:14:46Z", "lastUpdate": "2019-09-04T08:37:32Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "MEME Suite", "description": "Unified portal for discovery and analysis of sequence motifs (e.g. DNA binding sites, protein interaction domains). Motifs with/without gaps may be discovered, searched for in DNA and protein databases, compared to other motifs and analyzed for putative function by association with gene ontology terms. MEME is a tool designed for discovering and searching for DNA motifs such as transcription factor binding sites (TFBS) or protein domains.", "homepage": "http://meme-suite.org/", "biotoolsID": "meme_suite", "biotoolsCURIE": "biotools:meme_suite", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0238", "term": "Sequence motif discovery" } ], "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_1353", "term": "Sequence motif" }, "format": [ { "uri": "http://edamontology.org/format_2332", "term": "XML" }, { "uri": "http://edamontology.org/format_2331", "term": "HTML" }, { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "note": "MEME is a tool for discovering motifs in a group of related DNA or protein sequences. Note that MEME does not attempt to detect the alphabet from the sequences so you should specify it with the -dna or -protein options.", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0238", "term": "Sequence motif discovery" }, { "uri": "http://edamontology.org/operation_0415", "term": "Nucleic acid feature detection" }, { "uri": "http://edamontology.org/operation_2575", "term": "Protein binding site prediction" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1353", "term": "Sequence motif" }, "format": [ { "uri": "http://edamontology.org/format_1360", "term": "meme-motif" } ] }, { "data": { "uri": "http://edamontology.org/data_1234", "term": "Sequence set (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2048", "term": "Report" }, "format": [ { "uri": "http://edamontology.org/format_2331", "term": "HTML" } ] } ], "note": "MEME-ChIP performs several motif analysis steps on a set of DNA sequences that you provide. It is especially appropriate for analyzing the bound genomic regions identified in a transcription factor (TF) ChIP-seq experiment.MEME-ChIP can (1) discover novel DNA-binding motifs (with MEME and DREME), (2) determine which motifs are most centrally enriched (with CentriMo), (3) analyze them for similarity to known binding motifs (with Tomtom), and (4) automatically group the found motifs by similarity. A database of DNA motifs in MEME format. The immediate regions around individual ChIP-seq \"peaks\" from a transcription factor (TF) ChIP-seq experiment are ideal. MEME ChIP runs each program in its analysis in a different folder in the output directory. A summary file (index.html) is created in the output directory which lists the top motifs found and links to the results for each program.", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0238", "term": "Sequence motif discovery" } ], "input": [ { "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_0850", "term": "Sequence set" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1353", "term": "Sequence motif" }, "format": [ { "uri": "http://edamontology.org/format_2332", "term": "XML" }, { "uri": "http://edamontology.org/format_2331", "term": "HTML" }, { "uri": "http://edamontology.org/format_1360", "term": "meme-motif" } ] } ], "note": "DREME (Discriminative Regular Expression Motif Elicitation) finds relatively short motifs (up to 8 bases) fast, and can perform discriminative motif discovery if given a negative set, consisting of sequences unlikely to contain a motif of interest that is however likely to be found in the main (\"positive\") sequence set. The sequences should all be approximately the same length. If these sequences are not supplied then the program will shuffle the positive sequences and use that set for the negative sequences. DREME writes an XML file to the output folder and converts it into a minimal MEME-formatted motif file and a human readable html file.", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0238", "term": "Sequence motif discovery" }, { "uri": "http://edamontology.org/operation_0415", "term": "Nucleic acid feature detection" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1255", "term": "Sequence features" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_0850", "term": "Sequence set" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1353", "term": "Sequence motif" }, "format": [ { "uri": "http://edamontology.org/format_2331", "term": "HTML" }, { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "note": "GLAM2 is a program for finding motifs in sequences, typically amino-acid or nucleotide sequences. The main innovation of GLAM2 is that it allows insertions and deletions in motifs. The Alphabet of the sequences. This can be 'p' for protein sequences, 'n' for nucleotide sequences or the name of an GLAM2 alphabet file. A file containing FASTA formatted sequences.", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3501", "term": "Enrichment analysis" }, { "uri": "http://edamontology.org/operation_2238", "term": "Statistical calculation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3494", "term": "DNA sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_2070", "term": "Sequence motif (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_1360", "term": "meme-motif" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0951", "term": "Statistical estimate score" }, "format": [ { "uri": "http://edamontology.org/format_2331", "term": "HTML" }, { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "note": "AME (Analysis of Motif Enrichment) scores a set of DNA sequences given a set of DNA-binding motifs, treating each subsequence (and its reverse complement) in the sequence as a possible match to the motif. The sequences must be sorted by increasing value of some secondary criterion (e.g., expression level, peak height, fluorescence score). More than one file can be specified.", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0300", "term": "Sequence profile alignment" }, { "uri": "http://edamontology.org/operation_3501", "term": "Enrichment analysis" }, { "uri": "http://edamontology.org/operation_0337", "term": "Visualisation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1353", "term": "Sequence motif" }, "format": [ { "uri": "http://edamontology.org/format_1360", "term": "meme-motif" } ] }, { "data": { "uri": "http://edamontology.org/data_1234", "term": "Sequence set (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0869", "term": "Sequence-profile alignment" }, "format": [ { "uri": "http://edamontology.org/format_2331", "term": "HTML" }, { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "note": "CentriMo takes a set of motifs and a set of equal-length DNA or RNA sequences and plots the positional distribution of the best match of each motif. Ideally all of the same length. CentriMo outputs an HTML file that allows interactive selection of which motifs to plot the positional distribution for and control over smoothing and other plotting parameters.", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0445", "term": "Transcription factor binding site prediction" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1234", "term": "Sequence set (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_2070", "term": "Sequence motif (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_1360", "term": "meme-motif" } ] }, { "data": { "uri": "http://edamontology.org/data_2070", "term": "Sequence motif (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_1360", "term": "meme-motif" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2048", "term": "Report" }, "format": [ { "uri": "http://edamontology.org/format_2332", "term": "XML" }, { "uri": "http://edamontology.org/format_2331", "term": "HTML" } ] } ], "note": "SpaMo does inference of transcription factor complexes by looking for significant spacings between binding sites. This would typically be generated by expanding either side of a ChIP-seq peak to obtain sequences of about 500 bases in length. The primary motif is the motif for which you are trying to find cofactors. One or more MEME formatted motif files containing DNA motifs. The secondary motifs are tested for a significant spacing with the primary motif which might imply they act together.", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0226", "term": "Annotation" }, { "uri": "http://edamontology.org/operation_3501", "term": "Enrichment analysis" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0582", "term": "Ontology" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1772", "term": "Score" }, "format": [ { "uri": "http://edamontology.org/format_2332", "term": "XML" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2048", "term": "Report" }, "format": [ { "uri": "http://edamontology.org/format_2332", "term": "XML" }, { "uri": "http://edamontology.org/format_2331", "term": "HTML" } ] } ], "note": "The name GOMO stands for \"Gene Ontology for Motifs.\" The program searches in a set of ranked genes for enriched GO terms associated with high ranking genes. In other words, it identifies possible roles (Gene Ontology terms) for DNA binding motifs. A collection of GO terms mapped to to the sequences in the scoring file A XML file which contains for each motif the sequences and their score. By default GOMO calculates the ranksum statistics on the p-values of each gene given in the CisML input file.", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3438", "term": "Calculation" }, { "uri": "http://edamontology.org/operation_0239", "term": "Sequence motif recognition" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0850", "term": "Sequence set" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2048", "term": "Report" }, "format": [] } ], "note": "The name FIMO stands for \"Find Individual Motif Occurences.\" The program searches a database of DNA or protein sequences for occurrences of known motifs, treating each motif independently. See documentation for more details.", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0300", "term": "Sequence profile alignment" }, { "uri": "http://edamontology.org/operation_0338", "term": "Sequence database search" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1353", "term": "Sequence motif" }, "format": [ { "uri": "http://edamontology.org/format_1360", "term": "meme-motif" } ] }, { "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_0857", "term": "Sequence search results" }, "format": [ { "uri": "http://edamontology.org/format_2332", "term": "XML" }, { "uri": "http://edamontology.org/format_2331", "term": "HTML" } ] } ], "note": "MAST is a tool for searching biological sequence databases for sequences that contain one or more of a group of known motifs. MAST outputs three things: (1) The names of the high-scoring sequences sorted by the strength of the combined match of the sequence to all of the motifs in the group. (2) Motif diagrams showing the order and spacing of the motifs within each matching sequence. (3) Detailed annotation of each matching sequence showing the sequence and the locations and strengths of matches to the motifs.", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0291", "term": "Sequence clustering" }, { "uri": "http://edamontology.org/operation_0338", "term": "Sequence database search" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1353", "term": "Sequence motif" }, "format": [ { "uri": "http://edamontology.org/format_1360", "term": "meme-motif" } ] }, { "data": { "uri": "http://edamontology.org/data_1234", "term": "Sequence set (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2048", "term": "Report" }, "format": [] } ], "note": "MCAST searches a sequence database for statistically significant clusters of non-overlapping occurrences of a given set of motifs. See documentation for more details.", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0300", "term": "Sequence profile alignment" }, { "uri": "http://edamontology.org/operation_0338", "term": "Sequence database search" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1255", "term": "Sequence features" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1353", "term": "Sequence motif" }, "format": [] }, { "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_0857", "term": "Sequence search results" }, "format": [] } ], "note": "GLAM2SCAN finds matches, in a sequence database, to a motif discovered by GLAM2. Each match receives a score, indicating how well it fits the motif. The alphabet of the motif and sequences. This can be 'p' for protein sequences, 'n' for nucleotide sequences or the name of an GLAM2 alphabet file. A file containing a GLAM2 motif.", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_2421", "term": "Database search" }, { "uri": "http://edamontology.org/operation_0300", "term": "Sequence profile alignment" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1353", "term": "Sequence motif" }, "format": [ { "uri": "http://edamontology.org/format_1360", "term": "meme-motif" } ] }, { "data": { "uri": "http://edamontology.org/data_1353", "term": "Sequence motif" }, "format": [ { "uri": "http://edamontology.org/format_1360", "term": "meme-motif" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2080", "term": "Database search results" }, "format": [ { "uri": "http://edamontology.org/format_2331", "term": "HTML" }, { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "note": "The Tomtom program searches one or more query motifs against one or more databases of target motifs (and their DNA reverse complements), and reports for each query a list of target motifs, ranked by p-value. One or more files containing one or more motifs in MEME format.", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0361", "term": "Sequence annotation" }, { "uri": "http://edamontology.org/operation_2575", "term": "Protein binding site prediction" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1353", "term": "Sequence motif" }, "format": [ { "uri": "http://edamontology.org/format_1360", "term": "meme-motif" } ] }, { "data": { "uri": "http://edamontology.org/data_1234", "term": "Sequence set (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_1364", "term": "Hidden Markov model" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3002", "term": "Annotation track" }, "format": [ { "uri": "http://edamontology.org/format_2305", "term": "GFF" } ] } ], "note": "The name AMA stands for \"Average Motif Affinity\". The program scores a set of DNA sequences given a DNA-binding motif, treating each position in the sequence as a possible binding event. A file containing 0-order Markov Model in background model format such as produced by fasta-get-markov.", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3434", "term": "Conversion" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2854", "term": "Position-specific scoring matrix" }, "format": [ { "uri": "http://edamontology.org/format_3597", "term": "psd" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1353", "term": "Sequence motif" }, "format": [ { "uri": "http://edamontology.org/format_1360", "term": "meme-motif" } ] } ], "note": "Convert an BEEML matrix file into a MEME motif file suitable for use with MEME Suite programs.", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3434", "term": "Conversion" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2854", "term": "Position-specific scoring matrix" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1353", "term": "Sequence motif" }, "format": [ { "uri": "http://edamontology.org/format_1360", "term": "meme-motif" } ] } ], "note": "Read a CHEN matrix file and convert to MEME format. You may concatenate files for more than one motif.", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3434", "term": "Conversion" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1353", "term": "Sequence motif" }, "format": [ { "uri": "http://edamontology.org/format_1197", "term": "InChI" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1353", "term": "Sequence motif" }, "format": [ { "uri": "http://edamontology.org/format_1360", "term": "meme-motif" } ] } ], "note": "Convert an IUPAC motif into MEME motif format suitable for use with MEME Suite programs.", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3434", "term": "Conversion" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1353", "term": "Sequence motif" }, "format": [ { "uri": "http://edamontology.org/format_1367", "term": "JASPAR format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1353", "term": "Sequence motif" }, "format": [ { "uri": "http://edamontology.org/format_1360", "term": "meme-motif" } ] } ], "note": "Convert a directory of JASPAR files into a MEME motif suitable for use with MEME Suite programs.", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3434", "term": "Conversion" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1353", "term": "Sequence motif" }, "format": [ { "uri": "http://edamontology.org/format_1360", "term": "meme-motif" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1353", "term": "Sequence motif" }, "format": [ { "uri": "http://edamontology.org/format_1360", "term": "meme-motif" } ] } ], "note": "Convert and merge multiple MEME formatted files into a single minimal meme format file.", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3434", "term": "Conversion" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2854", "term": "Position-specific scoring matrix" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1353", "term": "Sequence motif" }, "format": [ { "uri": "http://edamontology.org/format_1360", "term": "meme-motif" } ] } ], "note": "Convert a nestedMICA (BioTiffin/XMS) matrix file into a MEME motif file suitable for use with MEME Suite programs.", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3434", "term": "Conversion" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2854", "term": "Position-specific scoring matrix" }, "format": [ { "uri": "http://edamontology.org/format_1915", "term": "Format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1353", "term": "Sequence motif" }, "format": [ { "uri": "http://edamontology.org/format_1360", "term": "meme-motif" } ] } ], "note": "Convert an PRIORITY matrix file into a MEME motif file suitable for use with MEME Suite programs.", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3434", "term": "Conversion" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1097", "term": "Sequence accession (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1353", "term": "Sequence motif" }, "format": [ { "uri": "http://edamontology.org/format_1360", "term": "meme-motif" } ] } ], "note": "Convert an RNA sequence to its binding motif in MEME motif format.", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3434", "term": "Conversion" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1361", "term": "Position frequency matrix" }, "format": [ { "uri": "http://edamontology.org/format_1915", "term": "Format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1353", "term": "Sequence motif" }, "format": [ { "uri": "http://edamontology.org/format_1360", "term": "meme-motif" } ] } ], "note": "Convert an SCPD matrix file into a MEME motif suitable for use with MEME Suite programs.", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3434", "term": "Conversion" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0850", "term": "Sequence set" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1353", "term": "Sequence motif" }, "format": [ { "uri": "http://edamontology.org/format_1360", "term": "meme-motif" } ] } ], "note": "Convert a directory of files containing sites into a MEME motif file suitable for use with MEME Suite programs.", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3434", "term": "Conversion" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2854", "term": "Position-specific scoring matrix" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1353", "term": "Sequence motif" }, "format": [ { "uri": "http://edamontology.org/format_1360", "term": "meme-motif" } ] } ], "note": "Convert a file containing the tab separated columns exported from the spreadsheet of Taipale results into MEME motif format. A Taipale file describes one or more motifs in terms of a probability matrix in column orientation.", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3434", "term": "Conversion" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1353", "term": "Sequence motif" }, "format": [ { "uri": "http://edamontology.org/format_1915", "term": "Format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1353", "term": "Sequence motif" }, "format": [ { "uri": "http://edamontology.org/format_1360", "term": "meme-motif" } ] } ], "note": "Convert a TAMO file into a MEME motif file suitable for use with MEME Suite programs. A TAMO file describes one or more motifs in terms of a Log-odds matrix and a set of sites that were used to make the motif.", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3434", "term": "Conversion" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2082", "term": "Matrix" }, "format": [ { "uri": "http://edamontology.org/format_1915", "term": "Format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1353", "term": "Sequence motif" }, "format": [ { "uri": "http://edamontology.org/format_1360", "term": "meme-motif" } ] } ], "note": "Convert a TRANSFAC 'matrix.dat' file into a MEME motif file suitable for use with MEME Suite programs.", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3434", "term": "Conversion" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2082", "term": "Matrix" }, "format": [ { "uri": "http://edamontology.org/format_1915", "term": "Format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1353", "term": "Sequence motif" }, "format": [ { "uri": "http://edamontology.org/format_1360", "term": "meme-motif" } ] } ], "note": "Converts UNIPROBE matricies from standard input into a MEME motif file suitable for use with MEME Suite programs. Can be several matricies.", "cmd": null }, { "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_1982", "term": "ClustalW format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0850", "term": "Sequence set" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "note": "This program converts a multiple alignment in clustalw format into a FASTA file.", "cmd": null }, { "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_1982", "term": "ClustalW format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0850", "term": "Sequence set" }, "format": [ { "uri": "http://edamontology.org/format_1997", "term": "PHYLIP format" } ] } ], "note": "This program converts a multiple alignment in ClustalW format into a PHYLIP file.", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3434", "term": "Conversion" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1353", "term": "Sequence motif" }, "format": [ { "uri": "http://edamontology.org/format_1915", "term": "Format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0850", "term": "Sequence set" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "note": "This program reads in a motif found by glam2, and writes it in a standard alignment format (FASTA-with-gaps or MSF). Choose to output sequences in FASTA-with-gaps or MSF. The output format depends on input parameter.", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3434", "term": "Conversion" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0582", "term": "Ontology" }, "format": [ { "uri": "http://edamontology.org/format_2196", "term": "OBO format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0582", "term": "Ontology" }, "format": [ { "uri": "http://edamontology.org/format_1915", "term": "Format" } ] } ], "note": "Convert a Gene Ontology OBO file into a GO DAG file.", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3434", "term": "Conversion" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0857", "term": "Sequence search results" }, "format": [ { "uri": "http://edamontology.org/format_2332", "term": "XML" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0857", "term": "Sequence search results" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "note": "Provides backwards compatibility by converting a mast xml file into a mast text file.", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0233", "term": "Sequence conversion" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2044", "term": "Sequence" }, "format": [ { "uri": "http://edamontology.org/format_1948", "term": "nbrf/pir" }, { "uri": "http://edamontology.org/format_1966", "term": "ASN.1 sequence format" }, { "uri": "http://edamontology.org/format_1962", "term": "strider format" }, { "uri": "http://edamontology.org/format_1964", "term": "plain text format (unformatted)" }, { "uri": "http://edamontology.org/format_1915", "term": "Format" }, { "uri": "http://edamontology.org/format_1925", "term": "codata" }, { "uri": "http://edamontology.org/format_1935", "term": "GCG" }, { "uri": "http://edamontology.org/format_1929", "term": "FASTA" }, { "uri": "http://edamontology.org/format_1997", "term": "PHYLIP format" }, { "uri": "http://edamontology.org/format_1927", "term": "EMBL format" }, { "uri": "http://edamontology.org/format_1954", "term": "Pearson format" }, { "uri": "http://edamontology.org/format_1912", "term": "Nexus format" }, { "uri": "http://edamontology.org/format_1936", "term": "GenBank format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2044", "term": "Sequence" }, "format": [ { "uri": "http://edamontology.org/format_1948", "term": "nbrf/pir" }, { "uri": "http://edamontology.org/format_1925", "term": "codata" }, { "uri": "http://edamontology.org/format_1962", "term": "strider format" }, { "uri": "http://edamontology.org/format_1915", "term": "Format" }, { "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_1934", "term": "fitch program" }, { "uri": "http://edamontology.org/format_1927", "term": "EMBL format" }, { "uri": "http://edamontology.org/format_1936", "term": "GenBank format" }, { "uri": "http://edamontology.org/format_1964", "term": "plain text format (unformatted)" }, { "uri": "http://edamontology.org/format_1912", "term": "Nexus format" }, { "uri": "http://edamontology.org/format_1954", "term": "Pearson format" }, { "uri": "http://edamontology.org/format_1966", "term": "ASN.1 sequence format" } ] } ], "note": "Converts protein and DNA sequence formats.", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_2995", "term": "Sequence classification" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2534", "term": "Sequence attribute" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1022", "term": "Sequence feature label" }, "format": [] } ], "note": "Classify a string passed as a command line argument as an instance of the DNA or protein alphabet. The letters of an unknown alphabet. The program prints 'DNA' or 'PROTEIN' to standard output, depending on the value of the alphabet argument.", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_2238", "term": "Statistical calculation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3002", "term": "Annotation track" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0951", "term": "Statistical estimate score" }, "format": [] } ], "note": "Read an AMA output file and output each sequence name, p-value and q-value. For each sequence in the input, outputs the sequence name, the p-value of the sequence and the q-value (minimum false discovery rate).", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3480", "term": "Probabilistic data generation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1353", "term": "Sequence motif" }, "format": [ { "uri": "http://edamontology.org/format_1360", "term": "meme-motif" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3466", "term": "EPS" }, { "uri": "http://edamontology.org/format_3604", "term": "svg" } ] } ], "note": "Create motif logos. A file containing one or more motifs in MEME format. Logo", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_2238", "term": "Statistical calculation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2854", "term": "Position-specific scoring matrix" }, "format": [ { "uri": "http://edamontology.org/format_1915", "term": "Format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0951", "term": "Statistical estimate score" }, "format": [] } ], "note": "compute-prior-dist computes the distribution of priors from a file in MEME PSP format. Number of increments to scale the distribution into. The first two lines are the minimum and maximum priors. Each succeeding line contains the probability that a prior is in the bin.", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_2426", "term": "Modelling and simulation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2044", "term": "Sequence" }, "format": [ { "uri": "http://edamontology.org/format_1940", "term": "giFASTA format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1364", "term": "Hidden Markov model" }, "format": [] } ], "note": "The program fasta-get-markov estimates a Markov model from a FASTA file of sequences.", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_1812", "term": "Loading" }, { "uri": "http://edamontology.org/operation_3096", "term": "Editing" } ], "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_2044", "term": "Sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "note": "Read and write FASTA files.", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3429", "term": "Generation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0850", "term": "Sequence set" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0850", "term": "Sequence set" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "note": "Create a random subset of the sequences in a FASTA formatted file.", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_2238", "term": "Statistical calculation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1772", "term": "Score" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2048", "term": "Report" }, "format": [ { "uri": "http://edamontology.org/format_1915", "term": "Format" } ] } ], "note": "fitevd fits an extreme value distribution to a set of score-length pairs. Reads white-space separated score-length pairs from standard input.", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0230", "term": "Sequence generation" } ], "input": [], "output": [ { "data": { "uri": "http://edamontology.org/data_2044", "term": "Sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "note": "gendb generates the specified number of sequences using a Markov model.", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0236", "term": "Sequence composition calculation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0850", "term": "Sequence set" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1255", "term": "Sequence features" }, "format": [] } ], "note": "The program getsize prints statistics about the FASTA sequences.", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0335", "term": "Formatting" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1353", "term": "Sequence motif" }, "format": [] }, { "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_2044", "term": "Sequence" }, "format": [] } ], "note": "This program masks a glam2 motif out of sequences, so that weaker motifs can be found. The GLAM2 motif to mask with 'x' in the sequences. The FASTA formatted sequences to mask. The input sequences are output with the GLAM2 motif sites masked out with 'x's.", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0226", "term": "Annotation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0582", "term": "Ontology" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2048", "term": "Report" }, "format": [ { "uri": "http://edamontology.org/format_2332", "term": "XML" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2048", "term": "Report" }, "format": [ { "uri": "http://edamontology.org/format_2332", "term": "XML" } ] } ], "note": "Updates the GOMO XML file(s) to add details about the GO terms, such as their name, hierarchy, relative position in that hierarchy and which are implied by others in the significant terms for each motif. A file containing the heirarchy of the GO terms in the format specified here. An XML file from GOMO to update. The GOMO XML File is updated to contain details about the GO terms heirarchy.", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0335", "term": "Formatting" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "format": [] } ], "output": [], "note": "Easily rename MEME Suite HTML files to unique names incorporating the path name (rather than 'meme.html'). The program takes the names of one or more output directories created by MEME Suite programs such as MEME, CENTRIMO etc.", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_2238", "term": "Statistical calculation" } ], "input": [ { "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_1353", "term": "Sequence motif" }, "format": [ { "uri": "http://edamontology.org/format_1360", "term": "meme-motif" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1772", "term": "Score" }, "format": [] } ], "note": "This utility calculates the statistical power of a phylogenetic motif model. Each line of the output has the following: Motif ID score score FPR False Positive Rate TPR True Positive Rate", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0238", "term": "Sequence motif discovery" } ], "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_2854", "term": "Position-specific scoring matrix" }, "format": [ { "uri": "http://edamontology.org/format_2200", "term": "FASTA-like (text)" } ] } ], "note": "Generate position-specific priors from positive (likely to contain a feature of interest) and negative (unlikely to contain a feature of interest) sequences for use as an additional input to MEME. A file containing FASTA formatted sequences which are to be used as the primary set in PSP calculation. A file containing FASTA formatted sequences which are to be used as the control set in PSP calculation. A FASTA-like PSP format is written to standard output, it contains a prior for every position of every sequence in the primary set.", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0369", "term": "Sequence cutting" } ], "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_2044", "term": "Sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "note": "Purge removes redundant sequences from a FASTA file. A file containing FASTA formatted sequences. This file will be overwritten. Purge overwrites the original FASTA sequence file with the purged sequences.", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_2238", "term": "Statistical calculation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1669", "term": "P-value" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0951", "term": "Statistical estimate score" }, "format": [] } ], "note": "Takes as input a list of p-values and prints a corresponding list of q-values, computed using the method of Benjamini and Hochberg. A tab separated file containing a column of p-values. Other columns may exist Outputs tab-delimited columns.", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_2424", "term": "Comparison" }, { "uri": "http://edamontology.org/operation_0324", "term": "Phylogenetic tree analysis" } ], "input": [ { "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_0863", "term": "Sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_1982", "term": "ClustalW format" } ] } ], "output": [ { "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_0863", "term": "Sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_1982", "term": "ClustalW format" } ] } ], "note": "Given a tree and an alignment, identify the intersection of the sets of sequence IDs and leaf labels. Trim the extra sequences and leaves and print the resulting alignment and tree.", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3081", "term": "Sequence alignment editing" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_1982", "term": "ClustalW format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [] } ], "note": "Extract specified range of columns from an alignment. The extracted region of the sequence alignment is written to standard output.", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3081", "term": "Sequence alignment editing" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1045", "term": "Species name" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_1982", "term": "ClustalW format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [] } ], "note": "Remove from an alignment all columns that contain a gap in the specified species. The name of a species present in the alignment for which gaps should be removed. The alignment, with the remaining columns that don't have gaps in the specified species, is written to standard output.", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0327", "term": "Phylogenetic footprinting / shadowing" } ], "input": [ { "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_0863", "term": "Sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_1982", "term": "ClustalW format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2523", "term": "Phylogenetic data" }, "format": [ { "uri": "http://edamontology.org/format_2332", "term": "XML" }, { "uri": "http://edamontology.org/format_2331", "term": "HTML" }, { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "note": "Perform phylogenetic shadowing on a given DNA alignment, using a given tree. This program is a simplified version of motiph, in which the equilibrium distribution is set equal to the background model, rather than being taken from a given motif. This tree may contain additional species not represented in the alignment.", "cmd": null } ], "toolType": [ "Command-line tool", "Web application", "Suite" ], "topic": [ { "uri": "http://edamontology.org/topic_0749", "term": "Transcription factors and regulatory sites" }, { "uri": "http://edamontology.org/topic_0203", "term": "Gene expression" }, { "uri": "http://edamontology.org/topic_3125", "term": "DNA binding sites" }, { "uri": "http://edamontology.org/topic_0736", "term": "Protein folds and structural domains" }, { "uri": "http://edamontology.org/topic_0160", "term": "Sequence sites, features and motifs" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "http://meme-suite.org/doc/overview.html?man_type=web", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": null, "pmid": "7584402", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Fitting a mixture model by expectation maximization to discover motifs in biopolymers.", "abstract": "The algorithm described in this paper discovers one or more motifs in a collection of DNA or protein sequences by using the technique of expectation maximization to fit a two-component finite mixture model to the set of sequences. Multiple motifs are found by fitting a mixture model to the data, probabilistically erasing the occurrences of the motif thus found, and repeating the process to find successive motifs. The algorithm requires only a set of unaligned sequences and a number specifying the width of the motifs as input. It returns a model of each motif and a threshold which together can be used as a Bayes-optimal classifier for searching for occurrences of the motif in other databases. The algorithm estimates how many times each motif occurs in each sequence in the dataset and outputs an alignment of the occurrences of the motif. The algorithm is capable of discovering several different motifs with differing numbers of occurrences in a single dataset.", "date": "1994-01-01T00:00:00Z", "citationCount": 3490, "authors": [ { "name": "Bailey T.L." }, { "name": "Elkan C." } ], "journal": "Proceedings / ... International Conference on Intelligent Systems for Molecular Biology ; ISMB. International Conference on Intelligent Systems for Molecular Biology" } }, { "doi": null, "pmid": "7584439", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "The value of prior knowledge in discovering motifs with MEME.", "abstract": "MEME is a tool for discovering motifs in sets of protein or DNA sequences. This paper describes several extensions to MEME which increase its ability to find motifs in a totally unsupervised fashion, but which also allow it to benefit when prior knowledge is available. When no background knowledge is asserted. MEME obtains increased robustness from a method for determining motif widths automatically, and from probabilistic models that allow motifs to be absent in some input sequences. On the other hand, MEME can exploit prior knowledge about a motif being present in all input sequences, about the length of a motif and whether it is a palindrome, and (using Dirichlet mixtures) about expected patterns in individual motif positions. Extensive experiments are reported which support the claim that MEME benefits from, but does not require, background knowledge. The experiments use seven previously studied DNA and protein sequence families and 75 of the protein families documented in the Prosite database of sites and patterns, Release 11.1.", "date": "1995-01-01T00:00:00Z", "citationCount": 531, "authors": [ { "name": "Bailey T.L." }, { "name": "Elkan C." } ], "journal": "Proceedings / ... International Conference on Intelligent Systems for Molecular Biology ; ISMB. International Conference on Intelligent Systems for Molecular Biology" } }, { "doi": null, "pmid": "8877500", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "The megaprior heuristic for discovering protein sequence patterns.", "abstract": "Several computer algorithms for discovering patterns in groups of protein sequences are in use that are based on fitting the parameters of a statistical model to a group of related sequences. These include hidden Markov model (HMM) algorithms for multiple sequence alignment, and the MEME and Gibbs sampler algorithms for discovering motifs. These algorithms are sometimes prone to producing models that are incorrect because two or more patients have been combined. The statistical model produced in this situation is a convex combination (weighted average) of two or more different models. This paper presents a solution to the problem of convex combinations in the form of a heuristic based on using extremely low variance Dirichlet mixture priors as part of the statistical model. This heuristic, which we call the megaprior heuristic, increase the strength (i.e., decreases the variance) of the prior in proportion to the size of the sequence dataset. This causes each column in the final model to strongly resemble the mean of a single component of the prior, regardless of the size of the dataset. We describe the cause of the convex combination problem, analyze it mathematically, motivate and describe the implementation of the megaprior heuristic, and show how it can effectively eliminate the problem of convex combinations in protein sequence pattern discovery.", "date": "1996-01-01T00:00:00Z", "citationCount": 25, "authors": [ { "name": "Bailey T.L." }, { "name": "Gribskov M." } ], "journal": "Proceedings / ... International Conference on Intelligent Systems for Molecular Biology ; ISMB. International Conference on Intelligent Systems for Molecular Biology" } }, { "doi": null, "pmid": "8902357", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Parameme: A parallel implementation and a web interface for a dna and protein motif discovery tool", "abstract": "Many advanced software tools fail to reach a wide audience because they require specialized hardware, installation expertise, or an abundance of CPU cycles. The worldwide web offers a new opportunity for distributing such systems. One such program, MEME, discovers repeated patterns, called motifs, in sets of DNA or protein sequences. This tool is now available to biologists over the worldwide web, using an asynchronous, single-program multiple-data version of the program called ParaMEME that runs on an Intel Paragon XP/S parallel computer at the San Diego Super-computer Center. ParaMEME scales gracefully to 64 nodes on the Paragon with efficiencies > 72% for large data sets. The worldwide web interface to ParaMEME accepts a set of sequences interactively from a user, submits the sequences to the Paragon for analysis, and e-mails the results back to the user. ParaMEME is available for free public use at http://www. sdsc. edu/CompSci/Biomed/ MEME. © 1996, Oxford University Press.", "date": "1996-01-01T00:00:00Z", "citationCount": 73, "authors": [ { "name": "Grundy W.N." }, { "name": "Bailey T.L." }, { "name": "Eikan C.P." } ], "journal": "Bioinformatics" } }, { "doi": null, "pmid": "9283754", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Meta-meme: Motif-based hidden markov models of protein families", "abstract": "Motivation: Modeling families of related biological sequences using Hidden Markov models (HMMs), although increasingly widespread, faces at least one major problem: because of the complexity of these mathematical models, they require a relatively large training set in order to accurately recognize a given family. For families in which there are few known sequences, a standard linear HMM contains too many parameters to be trained adequately Results: This work attempts to solve that problem by generating smaller HMMs which precisely model only the conserved regions of the family. These HMMs are constructed from motif models generated by the EM algorithm using the MEME software. Because motif-based HMMs have relatively few parameters, they can be trained using smaller data sets. Studies of short chain alcohol dehydrogenases and 4Fe-4S ferredoxins support the claim that motif-based HMMs exhibit increased sensitivity and selectivity in database searches, especially when training sets contain few sequences. Availability: http://www.sdsc.edu/MEME Contact: bgrundy@cs.ucsd.edu. © 1997, Oxford University Press.", "date": "1997-01-01T00:00:00Z", "citationCount": 154, "authors": [ { "name": "Grundy W.N." }, { "name": "Bailey T.L." }, { "name": "Baker M.E." }, { "name": "Eikan C.P." } ], "journal": "Bioinformatics" } }, { "doi": null, "pmid": "9366496", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "An artificial intelligence approach to motif discovery in protein sequences: Application to steroid dehydrogenases", "abstract": "MEME (Multiple Expectation-maximization for Motif Elicitation) is a unique new software tool that uses artificial intelligence techniques to discover motifs shared by a set of protein sequences in a fully automated manner. This paper is the first detailed study of the use of MEME to analyse a large, biologically relevant set of sequences, and to evaluate the sensitivity and accuracy of MEME in identifying structurally important motifs. For this purpose, we chose the short-chain alcohol dehydrogenase superfamily because it is large and phylogenetically diverse, providing a test of how well MEME can work on sequences with low amino acid similarity. Moreover, this dataset contains enzymes of biological importance, and because several enzymes have known X-ray crystallographic structures, we can test the usefulness of MEME for structural analysis. The first six motifs from MEME map onto structurally important cl-helices and β-strands on Streptomyces hydrogenans 20β-hydroxysteroid dehydrogenase. We also describe MAST (Motif Alignment Search Tool), which conveniently uses output: from MEME for searching databases such as SWISS-PROT and Genpept. MAST provides statistical measures that hermit a rigorous evaluation of the significance of database searches with individual motifs or groups of motifs. A database search of Genpept90 by MAST with the log-odds matrix of the first six motifs obtained from MEME yields a bimodal output, demonstrating. the selectivity of MAST. We show for the first time, using primary sequence analysis, that bacterial sugar epimerases are homologs of short-chain dehydrogenases. MEME and MAST will be increasingly useful as genome sequencing provides large datasets of phylogenetically divergent sequences of biomedical interest.", "date": "1997-05-01T00:00:00Z", "citationCount": 55, "authors": [ { "name": "Bailey T.L." }, { "name": "Baker M.E." }, { "name": "Elkan C.P." } ], "journal": "Journal of Steroid Biochemistry and Molecular Biology" } }, { "doi": null, "pmid": "16845028", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "MEME: Discovering and analyzing DNA and protein sequence motifs", "abstract": "MEME (Multiple EM for Motif Elicitation) is one of the most widely used tools for searching for novel 'signals' in sets of biological sequences. Applications include the discovery of new transcription factor binding sites and protein domains. MEME works by searching for repeated, ungapped sequence patterns that occur in the DNA or protein sequences provided by the user. Users can perform MEME searches via the web server hosted by the National Biomedical Computation Resource (http://meme. nbcr.net) and several mirror sites. Through the same web server, users can also access the Motif Alignment and Search Tool to search sequence databases for matches to motifs encoded in several popular formats. By clicking on buttons in the MEME output, users can compare the motifs discovered in their input sequences with databases of known motifs, search sequence databases for matches to the motifs and display the motifs in various formats. This article describes the freely accessible web server and its architecture, and discusses ways to use MEME effectively to find new sequence patterns in biological sequences and analyze their significance. © The Author 2006. Published by Oxford University Press. All rights reserved.", "date": "2006-07-01T00:00:00Z", "citationCount": 1542, "authors": [ { "name": "Bailey T.L." }, { "name": "Williams N." }, { "name": "Misleh C." }, { "name": "Li W.W." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/nar/gkp335", "pmid": "19458158", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "MEME Suite: Tools for motif discovery and searching", "abstract": "The MEME Suite web server provides a unified portal for online discovery and analysis of sequence motifs representing features such as DNA binding sites and protein interaction domains. The popular MEME motif discovery algorithm is now complemented by the GLAM2 algorithm which allows discovery of motifs containing gaps. Three sequence scanning algorithms - MAST, FIMO and GLAM2SCAN - allow scanning numerous DNA and protein sequence databases for motifs discovered by MEME and GLAM2. Transcription factor motifs (including those discovered using MEME) can be compared with motifs in many popular motif databases using the motif database scanning algorithm Tomtom. Transcription factor motifs can be further analyzed for putative function by association with Gene Ontology (GO) terms using the motif-GO term association tool GOMO. MEME output now contains sequence LOGOS for each discovered motif, as well as buttons to allow motifs to be conveniently submitted to the sequence and motif database scanning algorithms (MAST, FIMO and Tomtom), or to GOMO, for further analysis. GLAM2 output similarly contains buttons for further analysis using GLAM2SCAN and for rerunning GLAM2 with different parameters. All of the motif-based tools are now implemented as web services via Opal. Source code, binaries and a web server are freely available for noncommercial use at http://meme.nbcr.net.", "date": "2009-08-04T00:00:00Z", "citationCount": 4500, "authors": [ { "name": "Bailey T.L." }, { "name": "Boden M." }, { "name": "Buske F.A." }, { "name": "Frith M." }, { "name": "Grant C.E." }, { "name": "Clementi L." }, { "name": "Ren J." }, { "name": "Li W.W." }, { "name": "Noble W.S." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "MEME Suite Support", "email": "meme-suite@uw.edu", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "community": null, "owner": "ELIXIR-EE", "additionDate": "2017-02-10T14:15:59Z", "lastUpdate": "2019-02-04T13:59:48Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "SPARSE", "description": "Very efficient structure-based alignment of RNAs.", "homepage": "http://www.bioinf.uni-freiburg.de/Software/SPARSE", "biotoolsID": "sparse", "biotoolsCURIE": "biotools:sparse", "version": [ "1.8.9" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0294", "term": "Structure-based sequence alignment" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3495", "term": "RNA sequence" }, "format": [ { "uri": "http://edamontology.org/format_2200", "term": "FASTA-like (text)" }, { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1916", "term": "Alignment" }, "format": [ { "uri": "http://edamontology.org/format_1982", "term": "ClustalW format" }, { "uri": "http://edamontology.org/format_3508", "term": "PDF" }, { "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_1465", "term": "RNA structure" }, "format": [ { "uri": "http://edamontology.org/format_3466", "term": "EPS" } ] } ], "note": "A simultaneous alignment and folding tool with quadratic complexity", "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0097", "term": "Nucleic acid structure analysis" }, { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" } ], "operatingSystem": [ "Linux", "Mac" ], "language": [ "Python" ], "license": "GPL-3.0", "collectionID": [ "de.NBI" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "http://www.bioinf.uni-freiburg.de/Software/SPARSE/", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btv185", "pmid": "25838465", "pmcid": "PMC4514930", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "SPARSE: Quadratic time simultaneous alignment and folding of RNAs without sequence-based heuristics", "abstract": "© The Author 2015. Published by Oxford University Press.Motivation: RNA-Seq experiments have revealed a multitude of novel ncRNAs. The gold standard for their analysis based on simultaneous alignment and folding suffers from extreme time complexity of O(n6). Subsequently, numerous faster 'Sankoff-style' approaches have been suggested. Commonly, the performance of such methods relies on sequence-based heuristics that restrict the search space to optimal or near-optimal sequence alignments; however, the accuracy of sequencebased methods breaks down for RNAs with sequence identities below 60%. Alignment approaches like LocARNAthat do not require sequence-based heuristics, have been limited to high complexity (> quartictime). Results: Breaking this barrier, we introduce the novel Sankoff-style algorithm 'sparsified prediction and alignment of RNAs based on their structure ensembles (SPARSE)', which runs in quadratic time without sequence-based heuristics. To achieve this low complexity, on par with sequence alignment algorithms, SPARSE features strong sparsification based on structural properties of the RNA ensembles. Following PMcomp, SPARSE gains further speed-up from lightweight energy computation. Although all existing lightweight Sankoff-style methods restrict Sankoff's original model by disallowing loop deletions and insertions, SPARSE transfers the Sankoff algorithm to the lightweight energy model completely for the first time. Compared with LocARNA, SPARSE achieves similar alignment and better folding quality in significantly less time (speedup: 3.7). At similar run-time, it aligns low sequence identity instances substantially more accurate than RAF, which uses sequence-based heuristics.", "date": "2015-08-01T00:00:00Z", "citationCount": 24, "authors": [ { "name": "Will S." }, { "name": "Otto C." }, { "name": "Miladi M." }, { "name": "Mohl M." }, { "name": "Backofen R." } ], "journal": "Bioinformatics" } } ], "credit": [ { "name": "Milad Miladi", "email": "miladim@informatik.uni-freiburg.de", "url": null, "orcidid": "http://orcid.org/0000-0002-0173-3009", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Sebastian Will", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Contributor" ], "note": null }, { "name": "University Freiburg", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "rnateam", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Rolf Backofen", "email": "rna@rna.informatik.uni-freiburg.de", "url": null, "orcidid": "http://orcid.org/0000-0001-8231-3323", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Developer" ], "note": null }, { "name": "Sebastian Will", "email": "will@bioinf.uni-leipzig.de", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Developer" ], "note": null }, { "name": "Rolf Backofen", "email": "rna@rna.informatik.uni-freiburg.de", "url": null, "orcidid": "http://orcid.org/0000-0001-8231-3323", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Sebastian Will", "email": "will@bioinf.uni-leipzig.de", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "community": null, "owner": "rnateam", "additionDate": "2016-04-29T09:58:49Z", "lastUpdate": "2019-01-11T00:33:45Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "ExpaRNA-P", "description": "Simultaneous exact pattern matching and folding of RNAs.", "homepage": "http://www.bioinf.uni-freiburg.de/Software/ExpaRNA-P/", "biotoolsID": "exparna-p", "biotoolsCURIE": "biotools:exparna-p", "version": [ "1.8.9" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0294", "term": "Structure-based sequence alignment" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3495", "term": "RNA sequence" }, "format": [ { "uri": "http://edamontology.org/format_2200", "term": "FASTA-like (text)" }, { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1916", "term": "Alignment" }, "format": [ { "uri": "http://edamontology.org/format_1982", "term": "ClustalW format" } ] }, { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3466", "term": "EPS" } ] } ], "note": "ExpaRNA is a fast, motif-based comparison and alignment tool for RNA molecules. It computes the best arrangement of local sequence-structure (substructure) motifs common to two RNAs.", "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/topic_0097", "term": "Nucleic acid structure analysis" } ], "operatingSystem": [ "Linux", "Mac" ], "language": [], "license": "GPL-3.0", "collectionID": [ "de.NBI" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "http://www.bioinf.uni-freiburg.de/Software/ExpaRNA-P/", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1186/s12859-014-0404-0", "pmid": "25551362", "pmcid": "PMC4302096", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "ExpaRNA-P: Simultaneous exact pattern matching and folding of RNAs", "abstract": "© Otto et al.; licensee BioMed Central.Background: Identifying sequence-structure motifs common to two RNAs can speed up the comparison of structural RNAs substantially. The core algorithm of the existent approach solves this problem for input structures. However, such structures are rarely known; moreover, predicting them computationally is no rescue, since single sequence structure prediction is highly unreliable. Results: The novel algorithm computes exactly matching sequence-structure motifs in entire Boltzmann-distributed structure ensembles of two RNAs; thereby we match and fold RNAs simultaneously, analogous to the well-known \"simultaneous alignment and folding\" of RNAs. While this implies much higher flexibility compared to, has the same very low complexity (quadratic in time and space), which is enabled by its novel structure ensemble-based sparsification. Furthermore, we devise a generalized chaining algorithm to compute compatible subsets of 's sequence-structure motifs. Resulting in the very fast RNA alignment approach, we utilize the best chain as anchor constraints for the sequence-structure alignment tool. is benchmarked in several variants and versus state-of-the-art approaches. In particular, we formally introduce and evaluate strict and relaxed variants of the problem; the latter makes the approach sensitive to compensatory mutations. Across a benchmark set of typical non-coding RNAs, has similar accuracy to but is four times faster (in both variants), while it achieves a speed-up over 30-fold for the longest benchmark sequences (≈400nt). Finally, different variants enable tailoring of the method to specific application scenarios. and are distributed as part of the package. The source code is freely available at. Conclusions: 's novel ensemble-based sparsification reduces its complexity to quadratic time and space. Thereby, significantly speeds up sequence-structure alignment while maintaining the alignment quality. Different variants support a wide range of applications.", "date": "2014-12-31T00:00:00Z", "citationCount": 12, "authors": [ { "name": "Otto C." }, { "name": "Mohl M." }, { "name": "Heyne S." }, { "name": "Amit M." }, { "name": "Landau G.M." }, { "name": "Backofen R." }, { "name": "Will S." } ], "journal": "BMC Bioinformatics" } } ], "credit": [ { "name": "University Freiburg", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "rnateam", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Rolf Backofen", "email": "rna@rna.informatik.uni-freiburg.de", "url": null, "orcidid": "http://orcid.org/0000-0001-8231-3323", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Developer" ], "note": null }, { "name": "Christina Otto", "email": "schmiedc@informatik.uni-freiburg.de", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Rolf Backofen", "email": "rna@rna.informatik.uni-freiburg.de", "url": null, "orcidid": "http://orcid.org/0000-0001-8231-3323", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Christina Otto", "email": "schmiedc@informatik.uni-freiburg.de", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "community": null, "owner": "rnateam", "additionDate": "2016-04-29T09:57:28Z", "lastUpdate": "2019-01-11T00:06:26Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "CARNA web server", "description": "Alignment of RNA structure ensembles.", "homepage": "http://rna.informatik.uni-freiburg.de/CARNA/", "biotoolsID": "carna", "biotoolsCURIE": "biotools:carna", "version": [ "1.2.5" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0294", "term": "Structure-based sequence alignment" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3495", "term": "RNA sequence" }, "format": [ { "uri": "http://edamontology.org/format_2200", "term": "FASTA-like (text)" }, { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3547", "term": "Image format" }, { "uri": "http://edamontology.org/format_3466", "term": "EPS" }, { "uri": "http://edamontology.org/format_3508", "term": "PDF" } ] }, { "data": { "uri": "http://edamontology.org/data_1916", "term": "Alignment" }, "format": [ { "uri": "http://edamontology.org/format_1982", "term": "ClustalW 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_2044", "term": "Sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "note": "CARNA requires only the RNA sequences as input and will compute base pair probability matrices and align the sequences based on their full ensembles of structures.", "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/topic_0097", "term": "Nucleic acid structure analysis" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [ "de.NBI" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "http://rna.informatik.uni-freiburg.de/Help.jsp", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gks491", "pmid": "22689637", "pmcid": "PMC3394245", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "CARNA-alignment of RNA structure ensembles", "abstract": "Due to recent algorithmic progress, tools for the gold standard of comparative RNA analysis, namely Sankoff-style simultaneous alignment and folding, are now readily applicable. Such approaches, however, compare RNAs with respect to a simultaneously predicted, single, nested consensus structure. To make multiple alignment of RNAs available in cases, where this limitation of the standard approach is critical, we introduce a web server that provides a complete and convenient interface to the RNA structure alignment tool 'CARNA'. This tool uniquely supports RNAs with multiple conserved structures per RNA and aligns pseudoknots intrinsically; these features are highly desirable for aligning riboswitches, RNAs with conserved folding pathways, or pseudoknots. We represent structural input and output information as base pair probability dot plots; this provides large flexibility in the input, ranging from fixed structures to structure ensembles, and enables immediate visual analysis of the results. In contrast to conventional Sankoff-style approaches, 'CARNA' optimizes all structural similarities in the input simultaneously, for example across an entire RNA structure ensemble. Even compared with already costly Sankoff-style alignment, 'CARNA' solves an intrinsically much harder problem by applying advanced, constraint-based, algorithmic techniques. Although 'CARNA' is specialized to the alignment of RNAs with several conserved structures, its performance on RNAs in general is on par with state-of-the-art general-purpose RNA alignment tools, as we show in a Bralibase 2.1 benchmark. The web server is freely available at http://rna.informatik.uni-freiburg.de/CARNA. © 2012 The Author(s).", "date": "2012-07-01T00:00:00Z", "citationCount": 18, "authors": [ { "name": "Sorescu D.A." }, { "name": "Mohl M." }, { "name": "Mann M." }, { "name": "Backofen R." }, { "name": "Will S." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "University Freiburg", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "rnateam", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Rolf Backofen", "email": "rna@rna.informatik.uni-freiburg.de", "url": null, "orcidid": "http://orcid.org/0000-0001-8231-3323", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Sebastian Will", "email": "will@bioinf.uni-leipzig.de", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Rolf Backofen", "email": "rna@rna.informatik.uni-freiburg.de", "url": null, "orcidid": "http://orcid.org/0000-0001-8231-3323", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Sebastian Will", "email": "will@bioinf.uni-leipzig.de", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "community": null, "owner": "rnateam", "additionDate": "2016-04-29T10:12:35Z", "lastUpdate": "2019-01-09T15:29:49Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null } ] }
