{"id":"https://openalex.org/W2129977376","doi":"https://doi.org/10.1093/bioinformatics/bts654","title":"DLocalMotif: a discriminative approach for discovering local motifs in protein sequences","display_name":"DLocalMotif: a discriminative approach for discovering local motifs in protein sequences","publication_year":2012,"publication_date":"2012-11-09","ids":{"openalex":"https://openalex.org/W2129977376","doi":"https://doi.org/10.1093/bioinformatics/bts654","mag":"2129977376","pmid":"https://pubmed.ncbi.nlm.nih.gov/23142965"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bts654","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts654","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/1/39/49060222/bioinformatics_29_1_39.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/29/1/39/49060222/bioinformatics_29_1_39.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5015187102","display_name":"Ahmed M. Mehdi","orcid":"https://orcid.org/0000-0002-9300-2341"},"institutions":[{"id":"https://openalex.org/I165143802","display_name":"The University of Queensland","ror":"https://ror.org/00rqy9422","country_code":"AU","type":"education","lineage":["https://openalex.org/I165143802"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Ahmed M. Mehdi","raw_affiliation_strings":["1 Institute for Molecular Bioscience, The University of Queensland, Australia, 2Microsoft corporation, USA, 3School of Chemistry and Molecular Biosciences, The University of Queensland, Australia and 4Infectious Diseases Research Centre, The University of Queensland, Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Institute for Molecular Bioscience, The University of Queensland, Australia, 2Microsoft corporation, USA, 3School of Chemistry and Molecular Biosciences, The University of Queensland, Australia and 4Infectious Diseases Research Centre, The University of Queensland, Australia","institution_ids":["https://openalex.org/I165143802"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5105463364","display_name":"Muhammad Shoaib B. Sehgal","orcid":null},"institutions":[{"id":"https://openalex.org/I165143802","display_name":"The University of Queensland","ror":"https://ror.org/00rqy9422","country_code":"AU","type":"education","lineage":["https://openalex.org/I165143802"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Muhammad Shoaib B. Sehgal","raw_affiliation_strings":["1 Institute for Molecular Bioscience, The University of Queensland, Australia, 2Microsoft corporation, USA, 3School of Chemistry and Molecular Biosciences, The University of Queensland, Australia and 4Infectious Diseases Research Centre, The University of Queensland, Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Institute for Molecular Bioscience, The University of Queensland, Australia, 2Microsoft corporation, USA, 3School of Chemistry and Molecular Biosciences, The University of Queensland, Australia and 4Infectious Diseases Research Centre, The University of Queensland, Australia","institution_ids":["https://openalex.org/I165143802"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053221368","display_name":"Bo\u0161tjan Kobe","orcid":"https://orcid.org/0000-0001-9413-9166"},"institutions":[{"id":"https://openalex.org/I165143802","display_name":"The University of Queensland","ror":"https://ror.org/00rqy9422","country_code":"AU","type":"education","lineage":["https://openalex.org/I165143802"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Bostjan Kobe","raw_affiliation_strings":["1 Institute for Molecular Bioscience, The University of Queensland, Australia, 2Microsoft corporation, USA, 3School of Chemistry and Molecular Biosciences, The University of Queensland, Australia and 4Infectious Diseases Research Centre, The University of Queensland, Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Institute for Molecular Bioscience, The University of Queensland, Australia, 2Microsoft corporation, USA, 3School of Chemistry and Molecular Biosciences, The University of Queensland, Australia and 4Infectious Diseases Research Centre, The University of Queensland, Australia","institution_ids":["https://openalex.org/I165143802"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017222669","display_name":"Timothy L. Bailey","orcid":"https://orcid.org/0000-0002-7018-9342"},"institutions":[{"id":"https://openalex.org/I165143802","display_name":"The University of Queensland","ror":"https://ror.org/00rqy9422","country_code":"AU","type":"education","lineage":["https://openalex.org/I165143802"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Timothy L. Bailey","raw_affiliation_strings":["1 Institute for Molecular Bioscience, The University of Queensland, Australia, 2Microsoft corporation, USA, 3School of Chemistry and Molecular Biosciences, The University of Queensland, Australia and 4Infectious Diseases Research Centre, The University of Queensland, Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Institute for Molecular Bioscience, The University of Queensland, Australia, 2Microsoft corporation, USA, 3School of Chemistry and Molecular Biosciences, The University of Queensland, Australia and 4Infectious Diseases Research Centre, The University of Queensland, Australia","institution_ids":["https://openalex.org/I165143802"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5045279138","display_name":"Mikael Bod\u00e9n","orcid":"https://orcid.org/0000-0003-3548-268X"},"institutions":[{"id":"https://openalex.org/I165143802","display_name":"The University of Queensland","ror":"https://ror.org/00rqy9422","country_code":"AU","type":"education","lineage":["https://openalex.org/I165143802"]}],"countries":["AU"],"is_corresponding":true,"raw_author_name":"Mikael Bod\u00e9n","raw_affiliation_strings":["1 Institute for Molecular Bioscience, The University of Queensland, Australia, 2Microsoft corporation, USA, 3School of Chemistry and Molecular Biosciences, The University of Queensland, Australia and 4Infectious Diseases Research Centre, The University of Queensland, Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Institute for Molecular Bioscience, The University of Queensland, Australia, 2Microsoft corporation, USA, 3School of Chemistry and Molecular Biosciences, The University of Queensland, Australia and 4Infectious Diseases Research Centre, The University of Queensland, Australia","institution_ids":["https://openalex.org/I165143802"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5045279138"],"corresponding_institution_ids":["https://openalex.org/I165143802"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":null,"fwci":0.6237,"has_fulltext":true,"cited_by_count":17,"citation_normalized_percentile":{"value":0.67060335,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"29","issue":"1","first_page":"39","last_page":"46"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.38659998774528503,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.38659998774528503,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.24950000643730164,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.2061000019311905,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/discriminative-model","display_name":"Discriminative model","score":0.9067018032073975},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6073525547981262},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6057325005531311},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4354642331600189},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.34004461765289307},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.32544898986816406},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2592776417732239}],"concepts":[{"id":"https://openalex.org/C97931131","wikidata":"https://www.wikidata.org/wiki/Q5282087","display_name":"Discriminative model","level":2,"score":0.9067018032073975},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6073525547981262},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6057325005531311},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4354642331600189},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.34004461765289307},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.32544898986816406},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2592776417732239}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020816","descriptor_name":"Amino Acid Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020816","descriptor_name":"Amino Acid Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020816","descriptor_name":"Amino Acid Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D021382","descriptor_name":"Protein Sorting Signals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D021382","descriptor_name":"Protein Sorting Signals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D021382","descriptor_name":"Protein Sorting Signals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/bts654","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts654","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/1/39/49060222/bioinformatics_29_1_39.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:23142965","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23142965","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:6636396","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6636396","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:espace.library.uq.edu.au:UQ:289993","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4306402388","display_name":"Queensland's institutional digital repository (The University of Queensland)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I165143802","host_organization_name":"The University of Queensland","host_organization_lineage":["https://openalex.org/I165143802"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Journal Article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bts654","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts654","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/1/39/49060222/bioinformatics_29_1_39.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/10","display_name":"Reduced inequalities","score":0.7400000095367432}],"awards":[],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2129977376.pdf","grobid_xml":"https://content.openalex.org/works/W2129977376.grobid-xml"},"referenced_works_count":45,"referenced_works":["https://openalex.org/W1532982760","https://openalex.org/W1548138800","https://openalex.org/W1867526322","https://openalex.org/W1966354073","https://openalex.org/W1969879558","https://openalex.org/W1975056515","https://openalex.org/W1976572901","https://openalex.org/W1979353384","https://openalex.org/W1990199254","https://openalex.org/W2011457803","https://openalex.org/W2012935774","https://openalex.org/W2014443494","https://openalex.org/W2015249729","https://openalex.org/W2019841176","https://openalex.org/W2030124080","https://openalex.org/W2033506551","https://openalex.org/W2034297330","https://openalex.org/W2036955572","https://openalex.org/W2043929240","https://openalex.org/W2061142076","https://openalex.org/W2080498142","https://openalex.org/W2086725260","https://openalex.org/W2097353028","https://openalex.org/W2097606916","https://openalex.org/W2106338117","https://openalex.org/W2109664412","https://openalex.org/W2113117122","https://openalex.org/W2115761267","https://openalex.org/W2127783584","https://openalex.org/W2141885858","https://openalex.org/W2145835877","https://openalex.org/W2155744824","https://openalex.org/W2157009395","https://openalex.org/W2158266834","https://openalex.org/W2160710283","https://openalex.org/W2162533342","https://openalex.org/W2163485494","https://openalex.org/W2165405501","https://openalex.org/W2170330565","https://openalex.org/W2177363367","https://openalex.org/W2414638960","https://openalex.org/W2610493035","https://openalex.org/W4210623056","https://openalex.org/W6655429099","https://openalex.org/W6715850260"],"related_works":["https://openalex.org/W2961085424","https://openalex.org/W2404514746","https://openalex.org/W4306674287","https://openalex.org/W1652783584","https://openalex.org/W2082783427","https://openalex.org/W3046775127","https://openalex.org/W3107602296","https://openalex.org/W3170094116","https://openalex.org/W4386462264","https://openalex.org/W4364306694"],"abstract_inverted_index":{"MOTIVATION:":[0],"Local":[1],"motifs":[2,39,148,170],"are":[3,41],"patterns":[4],"of":[5,64,77,97,111,127,141,153,162],"DNA":[6],"or":[7,22],"protein":[8,25,88],"sequences":[9,51],"that":[10,40,74,122,149,171,195],"occur":[11,150],"within":[12],"a":[13,18,56,125],"sequence":[14,201],"interval":[15],"relative":[16],"to":[17,35,53,106,118,135],"biologically":[19,37,199],"defined":[20],"anchor":[21],"landmark.":[23],"Current":[24],"motif":[26,85,98,129],"discovery":[27,86],"methods":[28,121],"do":[29],"not":[30,54],"adequately":[31],"consider":[32],"such":[33],"constraints":[34],"identify":[36],"significant":[38],"only":[42,124],"weakly":[43],"over-represented":[44],"but":[45],"spatially":[46],"confined.":[47],"Using":[48],"negatives,":[49],"i.e.":[50],"known":[52],"contain":[55],"local":[57,84],"motif,":[58],"can":[59],"further":[60],"increase":[61],"the":[62,71,109,133,154,181],"specificity":[63],"their":[65],"discovery.":[66],"RESULTS:":[67],"This":[68],"article":[69],"introduces":[70],"method":[72,115,134,182],"DLocalMotif":[73,90,196],"makes":[75],"use":[76,123],"positional":[78],"information":[79],"and":[80,101,188,193],"negative":[81,112],"data":[82],"for":[83],"in":[87],"sequences.":[89],"combines":[91],"three":[92],"scoring":[93],"functions,":[94],"measuring":[95],"degrees":[96],"over-representation,":[99],"entropy":[100],"spatial":[102],"confinement,":[103],"specifically":[104],"designed":[105],"discriminatively":[107],"exploit":[108],"availability":[110],"data.":[113],"The":[114,139,160],"is":[116],"shown":[117],"outperform":[119],"current":[120],"subset":[126],"these":[128],"characteristics.":[130],"We":[131,178],"apply":[132],"several":[136,146],"biological":[137],"datasets.":[138],"analysis":[140,161],"peroxisomal":[142,156],"targeting":[143,157],"signals":[144,166,187,192],"uncovers":[145,167],"novel":[147,169],"immediately":[151],"upstream":[152],"dominant":[155],"signal-1":[158],"signal.":[159],"proline-tyrosine":[163],"nuclear":[164,185],"localization":[165,186],"multiple":[168],"overlap":[172],"with":[173],"C2H2":[174],"zinc":[175],"finger":[176],"domains.":[177],"also":[179],"evaluate":[180],"on":[183],"classical":[184],"endoplasmic":[189],"reticulum":[190],"retention":[191],"find":[194],"successfully":[197],"recovers":[198],"relevant":[200],"properties.":[202],"AVAILABILITY:":[203],"http://bioinf.scmb.uq.edu.au/dlocalmotif/":[204]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":3},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":1}],"updated_date":"2026-08-26T07:47:46.906454","created_date":"2025-10-10T00:00:00"}
