{"name":"meme_fimo","description":"A software tool for scanning DNA or protein sequences with motifs described as position-specific scoring matrices.","homepage":"http://meme-suite.org/tools/meme","biotoolsID":"meme_fimo","biotoolsCURIE":"biotools:meme_fimo","version":["0.0.1"],"otherID":[],"relation":[],"function":[{"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_3092","term":"Protein feature detection"},{"uri":"http://edamontology.org/operation_2238","term":"Statistical calculation"}],"input":[{"data":{"uri":"http://edamontology.org/data_0006","term":"Data"},"format":[{"uri":"http://edamontology.org/format_2332","term":"XML"}]},{"data":{"uri":"http://edamontology.org/data_0863","term":"Sequence alignment"},"format":[{"uri":"http://edamontology.org/format_1929","term":"FASTA"}]},{"data":{"uri":"http://edamontology.org/data_0006","term":"Data"},"format":[{"uri":"http://edamontology.org/format_2330","term":"Textual format"}]}],"output":[{"data":{"uri":"http://edamontology.org/data_2048","term":"Report"},"format":[{"uri":"http://edamontology.org/format_2331","term":"HTML"}]},{"data":{"uri":"http://edamontology.org/data_0006","term":"Data"},"format":[{"uri":"http://edamontology.org/format_3475","term":"TSV"}]},{"data":{"uri":"http://edamontology.org/data_0006","term":"Data"},"format":[{"uri":"http://edamontology.org/format_3475","term":"TSV"}]},{"data":{"uri":"http://edamontology.org/data_0006","term":"Data"},"format":[{"uri":"http://edamontology.org/format_2332","term":"XML"}]},{"data":{"uri":"http://edamontology.org/data_0006","term":"Data"},"format":[{"uri":"http://edamontology.org/format_3475","term":"TSV"}]}],"note":null,"cmd":null}],"toolType":["Web application"],"topic":[{"uri":"http://edamontology.org/topic_0080","term":"Sequence analysis"},{"uri":"http://edamontology.org/topic_0199","term":"Genetic variation"},{"uri":"http://edamontology.org/topic_2269","term":"Statistics and probability"},{"uri":"http://edamontology.org/topic_3473","term":"Data mining"}],"operatingSystem":["Linux","Windows","Mac"],"language":[],"license":null,"collectionID":["galaxyPasteur","MEME"],"maturity":"Mature","cost":null,"accessibility":"Open access","elixirPlatform":[],"elixirNode":[],"elixirCommunity":[],"link":[{"url":"https://galaxy.pasteur.fr/tool_runner?tool_id=meme_fimo","type":["Galaxy service"],"note":null}],"download":[],"documentation":[{"url":"https://galaxy.pasteur.fr/root?tool_id=meme_fimo","type":["General"],"note":null}],"publication":[{"doi":"10.1093/bioinformatics/btr064","pmid":"21330290","pmcid":"PMC3065696","type":["Primary"],"version":null,"note":null,"metadata":{"title":"FIMO: Scanning for occurrences of a given motif","abstract":"Summary: A motif is a short DNA or protein sequence that contributes to the biological function of the sequence in which it resides. Over the past several decades, many computational methods have been described for identifying, characterizing and searching with sequence motifs. Critical to nearly any motif-based sequence analysis pipeline is the ability to scan a sequence database for occurrences of a given motif described by a position-specific frequency matrix.Results: We describe Find Individual Motif Occurrences (FIMO), a software tool for scanning DNA or protein sequences with motifs described as position-specific scoring matrices. The program computes a log-likelihood ratio score for each position in a given sequence database, uses established dynamic programming methods to convert this score to a P-value and then applies false discovery rate analysis to estimate a q-value for each position in the given sequence. FIMO provides output in a variety of formats, including HTML, XML and several Santa Cruz Genome Browser formats. The program is efficient, allowing for the scanning of DNA sequences at a rate of 3.5 Mb/s on a single CPU. © The Author(s) 2011. Published by Oxford University Press.","date":"2011-01-01T00:00:00Z","citationCount":2615,"authors":[{"name":"Grant C.E."},{"name":"Bailey T.L."},{"name":"Noble W.S."}],"journal":"Bioinformatics"}},{"doi":"10.1093/nar/gkw343","pmid":"27137889","pmcid":"PMC4987906","type":["Other"],"version":null,"note":null,"metadata":{"title":"The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update","abstract":"High-throughput data production technologies, particularly ‘next-generation’ DNA sequencing, have ushered in widespread and disruptive changes to biomedical research. Making sense of the large datasets produced by these technologies requires sophisticated statistical and computational methods, as well as substantial computational power. This has led to an acute crisis in life sciences, as researchers without informatics training attempt to perform computation-dependent analyses. Since 2005, the Galaxy project has worked to address this problem by providing a framework that makes advanced computational tools usable by non experts. Galaxy seeks to make data-intensive research more accessible, transparent and reproducible by providing a Web-based environment in which users can perform computational analyses and have all of the details automatically tracked for later inspection, publication, or reuse. In this report we highlight recently added features enabling biomedical analyses on a large scale.","date":"2016-07-08T00:00:00Z","citationCount":1410,"authors":[{"name":"Afgan E."},{"name":"Baker D."},{"name":"van den Beek M."},{"name":"Blankenberg D."},{"name":"Bouvier D."},{"name":"Cech M."},{"name":"Chilton J."},{"name":"Clements D."},{"name":"Coraor N."},{"name":"Eberhard C."},{"name":"Gruning B."},{"name":"Guerler A."},{"name":"Hillman-Jackson J."},{"name":"Kuster G.V."},{"name":"Rasche E."},{"name":"Soranzo N."},{"name":"Turaga N."},{"name":"Taylor J."},{"name":"Nekrutenko A."},{"name":"Goecks J."}],"journal":"Nucleic Acids Research"}},{"doi":"10.7490/f1000research.1114334.1","pmid":null,"pmcid":null,"type":["Other"],"version":null,"note":null,"metadata":null}],"credit":[{"name":"Galaxy Support Team","email":"galaxy@pasteur.fr","url":null,"orcidid":null,"gridid":null,"rorid":null,"fundrefid":null,"typeEntity":"Person","typeRole":["Primary contact"],"note":null}],"owner":"hmenager","additionDate":"2016-12-19T14:30:16Z","lastUpdate":"2024-11-25T13:56:38.194545Z","editPermission":{"type":"group","authors":["ELIXIR-EE"]},"validated":1,"homepage_status":0,"elixir_badge":0,"confidence_flag":null}