{"id":"https://openalex.org/W2108478344","doi":"https://doi.org/10.1093/nar/gkt463","title":"RBPmotif: a web server for the discovery of sequence and structure preferences of RNA-binding proteins","display_name":"RBPmotif: a web server for the discovery of sequence and structure preferences of RNA-binding proteins","publication_year":2013,"publication_date":"2013-06-10","ids":{"openalex":"https://openalex.org/W2108478344","doi":"https://doi.org/10.1093/nar/gkt463","mag":"2108478344","pmid":"https://pubmed.ncbi.nlm.nih.gov/23754853"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkt463","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkt463","pdf_url":"https://academic.oup.com/nar/article-pdf/41/W1/W180/3871353/gkt463.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/nar/article-pdf/41/W1/W180/3871353/gkt463.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5074332682","display_name":"Hilal Kazan","orcid":"https://orcid.org/0000-0003-2461-4579"},"institutions":[{"id":"https://openalex.org/I4210100577","display_name":"Antalya Bilim University","ror":"https://ror.org/013sqra93","country_code":"TR","type":"education","lineage":["https://openalex.org/I4210100577"]},{"id":"https://openalex.org/I4210163979","display_name":"Antalya IVF","ror":"https://ror.org/05b8d3v21","country_code":"TR","type":"healthcare","lineage":["https://openalex.org/I4210163979"]}],"countries":["TR"],"is_corresponding":true,"raw_author_name":"Hilal Kazan","raw_affiliation_strings":["Department of Computer Engineering, Antalya International University, Antalya, 07190, Turkey. hilal.kazan@antalya.edu.tr","Department of Computer Engineering, Antalya International University, Antalya, 07190, Turkey"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Engineering, Antalya International University, Antalya, 07190, Turkey. hilal.kazan@antalya.edu.tr","institution_ids":["https://openalex.org/I4210100577","https://openalex.org/I4210163979"]},{"raw_affiliation_string":"Department of Computer Engineering, Antalya International University, Antalya, 07190, Turkey","institution_ids":["https://openalex.org/I4210100577"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5035010657","display_name":"Quaid Morris","orcid":"https://orcid.org/0000-0002-2760-6999"},"institutions":[{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Quaid Morris","raw_affiliation_strings":["Department of Computer Engineering, Antalya International University, Antalya, 07190, Turkey, 2 Department of Computer Science, University of Toronto, Toronto, ON M5S 2E4, Canada, 3 Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada and 4 Banting and Best Department of Medical Research, University of Toronto, Toronto, ON M5G 1L6, Canada","University of Toronto, Toronto, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Engineering, Antalya International University, Antalya, 07190, Turkey, 2 Department of Computer Science, University of Toronto, Toronto, ON M5S 2E4, Canada, 3 Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada and 4 Banting and Best Department of Medical Research, University of Toronto, Toronto, ON M5G 1L6, Canada","institution_ids":["https://openalex.org/I185261750"]},{"raw_affiliation_string":"University of Toronto, Toronto, Canada","institution_ids":["https://openalex.org/I185261750"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5074332682"],"corresponding_institution_ids":["https://openalex.org/I4210100577","https://openalex.org/I4210163979"],"apc_list":{"value":3992,"currency":"USD","value_usd":3992},"apc_paid":{"value":3992,"currency":"USD","value_usd":3992},"fwci":2.4739,"has_fulltext":true,"cited_by_count":26,"citation_normalized_percentile":{"value":0.89605626,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"41","issue":"W1","first_page":"W180","last_page":"W186"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9998999834060669,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9998999834060669,"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/T10604","display_name":"RNA Research and Splicing","score":0.9998999834060669,"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/T11482","display_name":"RNA modifications and cancer","score":0.9983000159263611,"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/biology","display_name":"Biology","score":0.7594397664070129},{"id":"https://openalex.org/keywords/web-server","display_name":"Web server","score":0.6569267511367798},{"id":"https://openalex.org/keywords/motif","display_name":"Motif (music)","score":0.612233579158783},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5888888835906982},{"id":"https://openalex.org/keywords/sequence-motif","display_name":"Sequence motif","score":0.5721791386604309},{"id":"https://openalex.org/keywords/rna-binding-protein","display_name":"RNA-binding protein","score":0.47215867042541504},{"id":"https://openalex.org/keywords/sequence-analysis","display_name":"Sequence analysis","score":0.4345484673976898},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.432834655046463},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.36198434233665466},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3206353783607483},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.24944832921028137},{"id":"https://openalex.org/keywords/the-internet","display_name":"The Internet","score":0.14106252789497375},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.13263311982154846},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.10276606678962708}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.7594397664070129},{"id":"https://openalex.org/C11392498","wikidata":"https://www.wikidata.org/wiki/Q11288","display_name":"Web server","level":3,"score":0.6569267511367798},{"id":"https://openalex.org/C32276052","wikidata":"https://www.wikidata.org/wiki/Q908349","display_name":"Motif (music)","level":2,"score":0.612233579158783},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5888888835906982},{"id":"https://openalex.org/C117745874","wikidata":"https://www.wikidata.org/wiki/Q901612","display_name":"Sequence motif","level":3,"score":0.5721791386604309},{"id":"https://openalex.org/C41282012","wikidata":"https://www.wikidata.org/wiki/Q3928341","display_name":"RNA-binding protein","level":4,"score":0.47215867042541504},{"id":"https://openalex.org/C61053724","wikidata":"https://www.wikidata.org/wiki/Q1154615","display_name":"Sequence analysis","level":3,"score":0.4345484673976898},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.432834655046463},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.36198434233665466},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3206353783607483},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.24944832921028137},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.14106252789497375},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.13263311982154846},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.10276606678962708},{"id":"https://openalex.org/C24890656","wikidata":"https://www.wikidata.org/wiki/Q82811","display_name":"Acoustics","level":1,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0}],"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":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016601","descriptor_name":"RNA-Binding Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D016601","descriptor_name":"RNA-Binding Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D016601","descriptor_name":"RNA-Binding Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059372","descriptor_name":"Nucleotide Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059372","descriptor_name":"Nucleotide Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059372","descriptor_name":"Nucleotide Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/nar/gkt463","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkt463","pdf_url":"https://academic.oup.com/nar/article-pdf/41/W1/W180/3871353/gkt463.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:23754853","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23754853","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":"Nucleic acids research","raw_type":"Journal Article"},{"id":"pmh:oai:europepmc.org:2686078","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3692078","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/nar/gkt463","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkt463","pdf_url":"https://academic.oup.com/nar/article-pdf/41/W1/W180/3871353/gkt463.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.7599999904632568,"display_name":"Reduced inequalities","id":"https://metadata.un.org/sdg/10"}],"awards":[{"id":"https://openalex.org/G1629195103","display_name":"The eukaryotic RNA-protein recognition code","funder_award_id":"125894_1","funder_id":"https://openalex.org/F4320334506","funder_display_name":"Canadian Institutes of Health Research"}],"funders":[{"id":"https://openalex.org/F4320334506","display_name":"Canadian Institutes of Health Research","ror":"https://ror.org/01gavpb45"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2108478344.pdf","grobid_xml":"https://content.openalex.org/works/W2108478344.grobid-xml"},"referenced_works_count":27,"referenced_works":["https://openalex.org/W1978883675","https://openalex.org/W1995224771","https://openalex.org/W2000359198","https://openalex.org/W2011368877","https://openalex.org/W2019381697","https://openalex.org/W2019522436","https://openalex.org/W2053758959","https://openalex.org/W2072470582","https://openalex.org/W2073858449","https://openalex.org/W2092896180","https://openalex.org/W2096378231","https://openalex.org/W2103777723","https://openalex.org/W2116835111","https://openalex.org/W2119342775","https://openalex.org/W2122679732","https://openalex.org/W2125741255","https://openalex.org/W2129216514","https://openalex.org/W2132863465","https://openalex.org/W2145091349","https://openalex.org/W2147946837","https://openalex.org/W2149480306","https://openalex.org/W2151994495","https://openalex.org/W2153140501","https://openalex.org/W2157825442","https://openalex.org/W2169636286","https://openalex.org/W4205097856","https://openalex.org/W6655548692"],"related_works":["https://openalex.org/W2073661767","https://openalex.org/W2380185347","https://openalex.org/W2370034659","https://openalex.org/W2159636084","https://openalex.org/W2117168988","https://openalex.org/W2103777723","https://openalex.org/W2610941444","https://openalex.org/W2527742233","https://openalex.org/W3165554045","https://openalex.org/W2805661590"],"abstract_inverted_index":{"RBPmotif":[0,32,179],"web":[1,180],"server":[2,181],"(http://www.rnamotif.org)":[3],"implements":[4],"tools":[5],"to":[6,22,88,142],"identify":[7,89],"binding":[8,52,103],"preferences":[9,53,59,104,190],"of":[10,17,30,36,57,97,105,113,119,125,156,159,171,174,186,191],"RNA-binding":[11],"proteins":[12],"(RBPs).":[13],"Given":[14],"a":[15,47,63,134,194],"set":[16],"sequences":[18,167],"that":[19,83],"are":[20,131],"known":[21],"be":[23],"bound":[24,139,164],"and":[25,54,92,108,165,168,188],"unbound":[26,146,166],"by":[27],"the":[28,69,78,101,106,109,123,126,150,154,160,183],"RBP":[29,107],"interest,":[31],"provides":[33],"two":[34],"types":[35],"analysis:":[37],"(i)":[38],"de":[39],"novo":[40,72],"motif":[41,67,73,86,130,161],"finding":[42,74],"when":[43,60],"there":[44,61],"is":[45,62,75],"no":[46],"priori":[48],"knowledge":[49],"on":[50],"RBP's":[51],"(ii)":[55],"analysis":[56,99,120,185],"structure":[58,93,115,136,157,189],"previously":[64,79,127],"identified":[65,128],"sequence":[66,91,129,187],"for":[68],"RBP.":[70],"De":[71],"performed":[76],"with":[77],"published":[80],"RNAcontext":[81],"algorithm":[82],"learns":[84],"discriminative":[85],"models":[87],"both":[90],"preferences.":[94,116,176],"The":[95],"results":[96,151],"this":[98],"include":[100],"inferred":[102],"added":[110],"predictive":[111],"value":[112],"incorporating":[114],"Second":[117],"type":[118],"investigates":[121],"whether":[122],"instances":[124,144,162],"enriched":[132],"in":[133,138,145],"particular":[135],"context":[137],"sequences,":[140],"relative":[141],"its":[143],"sequences.":[147],"On":[148],"completion,":[149],"page":[152],"shows":[153],"comparison":[155],"contexts":[158],"between":[163],"an":[169],"assessment":[170],"statistical":[172],"significance":[173],"detected":[175],"In":[177],"summary,":[178],"enables":[182],"concurrent":[184],"RBPs":[192],"through":[193],"user-friendly":[195],"interface.":[196]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":2},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":4},{"year":2014,"cited_by_count":7},{"year":2013,"cited_by_count":4}],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2025-10-10T00:00:00"}
