{"id":"https://openalex.org/W2137526645","doi":"https://doi.org/10.1093/bioinformatics/btm179","title":"Locomotif: from graphical motif description to RNA motif search","display_name":"Locomotif: from graphical motif description to RNA motif search","publication_year":2007,"publication_date":"2007-07-01","ids":{"openalex":"https://openalex.org/W2137526645","doi":"https://doi.org/10.1093/bioinformatics/btm179","mag":"2137526645","pmid":"https://pubmed.ncbi.nlm.nih.gov/17646322"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btm179","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btm179","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/23/13/i392/23705381/btm179.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/23/13/i392/23705381/btm179.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5052892130","display_name":"Janina Reeder","orcid":"https://orcid.org/0000-0002-6704-6754"},"institutions":[{"id":"https://openalex.org/I20121455","display_name":"Bielefeld University","ror":"https://ror.org/02hpadn98","country_code":"DE","type":"education","lineage":["https://openalex.org/I20121455"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Janina Reeder","raw_affiliation_strings":["Faculty of Technology, Bielefeld University, D-33615 Bielefeld, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Technology, Bielefeld University, D-33615 Bielefeld, Germany","institution_ids":["https://openalex.org/I20121455"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5112342016","display_name":"Jens Reeder","orcid":null},"institutions":[{"id":"https://openalex.org/I20121455","display_name":"Bielefeld University","ror":"https://ror.org/02hpadn98","country_code":"DE","type":"education","lineage":["https://openalex.org/I20121455"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Jens Reeder","raw_affiliation_strings":["Faculty of Technology, Bielefeld University, D-33615 Bielefeld, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Technology, Bielefeld University, D-33615 Bielefeld, Germany","institution_ids":["https://openalex.org/I20121455"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5086259996","display_name":"Robert Giegerich","orcid":null},"institutions":[{"id":"https://openalex.org/I20121455","display_name":"Bielefeld University","ror":"https://ror.org/02hpadn98","country_code":"DE","type":"education","lineage":["https://openalex.org/I20121455"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Robert Giegerich","raw_affiliation_strings":["Faculty of Technology, Bielefeld University, D-33615 Bielefeld, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Technology, Bielefeld University, D-33615 Bielefeld, Germany","institution_ids":["https://openalex.org/I20121455"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5086259996"],"corresponding_institution_ids":["https://openalex.org/I20121455"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":{"value":3989,"currency":"USD","value_usd":3989},"fwci":2.2655,"has_fulltext":true,"cited_by_count":43,"citation_normalized_percentile":{"value":0.88159823,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"23","issue":"13","first_page":"i392","last_page":"i400"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.968999981880188,"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":0.968999981880188,"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":0.00839999970048666,"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":0.005400000140070915,"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/motif","display_name":"Motif (music)","score":0.7625001668930054},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7429006695747375},{"id":"https://openalex.org/keywords/java","display_name":"Java","score":0.5792439579963684},{"id":"https://openalex.org/keywords/graphics","display_name":"Graphics","score":0.5145920515060425},{"id":"https://openalex.org/keywords/download","display_name":"Download","score":0.4970555603504181},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.4926043152809143},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.4477267563343048},{"id":"https://openalex.org/keywords/sequence-motif","display_name":"Sequence motif","score":0.4386964440345764},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.3347497582435608},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.33395424485206604},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.32783979177474976},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.27931469678878784},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.17290350794792175},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.15983113646507263},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.08758026361465454}],"concepts":[{"id":"https://openalex.org/C32276052","wikidata":"https://www.wikidata.org/wiki/Q908349","display_name":"Motif (music)","level":2,"score":0.7625001668930054},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7429006695747375},{"id":"https://openalex.org/C548217200","wikidata":"https://www.wikidata.org/wiki/Q251","display_name":"Java","level":2,"score":0.5792439579963684},{"id":"https://openalex.org/C21442007","wikidata":"https://www.wikidata.org/wiki/Q1027879","display_name":"Graphics","level":2,"score":0.5145920515060425},{"id":"https://openalex.org/C2780154274","wikidata":"https://www.wikidata.org/wiki/Q7126717","display_name":"Download","level":2,"score":0.4970555603504181},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.4926043152809143},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.4477267563343048},{"id":"https://openalex.org/C117745874","wikidata":"https://www.wikidata.org/wiki/Q901612","display_name":"Sequence motif","level":3,"score":0.4386964440345764},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.3347497582435608},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.33395424485206604},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.32783979177474976},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.27931469678878784},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.17290350794792175},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.15983113646507263},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.08758026361465454},{"id":"https://openalex.org/C24890656","wikidata":"https://www.wikidata.org/wiki/Q82811","display_name":"Acoustics","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"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":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btm179","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btm179","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/23/13/i392/23705381/btm179.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:17646322","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/17646322","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":"Evaluation Study"},{"id":"pmh:oai:pub.librecat.org:1593132","is_oa":false,"landing_page_url":"https://pub.uni-bielefeld.de/record/1593132","pdf_url":null,"source":{"id":"https://openalex.org/S4306401671","display_name":"PUB \u2013 Publications at Bielefeld University (Bielefeld University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I20121455","host_organization_name":"Bielefeld University","host_organization_lineage":["https://openalex.org/I20121455"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Reeder J, Reeder J, Giegerich R. Locomotif: from graphical motif description to RNA motif search. &lt;em&gt;Bioinformatics&lt;/em&gt;. 2007;23(13):I392-I400.","raw_type":"info:eu-repo/semantics/conferenceObject"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btm179","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btm179","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/23/13/i392/23705381/btm179.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320320879","display_name":"Deutsche Forschungsgemeinschaft","ror":"https://ror.org/018mejw64"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2137526645.pdf","grobid_xml":"https://content.openalex.org/works/W2137526645.grobid-xml"},"referenced_works_count":27,"referenced_works":["https://openalex.org/W87459262","https://openalex.org/W1543796220","https://openalex.org/W1658694352","https://openalex.org/W1917330597","https://openalex.org/W1965247733","https://openalex.org/W1976312746","https://openalex.org/W1987010534","https://openalex.org/W1990236382","https://openalex.org/W2009818318","https://openalex.org/W2024177760","https://openalex.org/W2030794182","https://openalex.org/W2033907622","https://openalex.org/W2039820890","https://openalex.org/W2040998144","https://openalex.org/W2042881722","https://openalex.org/W2047222805","https://openalex.org/W2080427769","https://openalex.org/W2080667183","https://openalex.org/W2088784401","https://openalex.org/W2101269698","https://openalex.org/W2105070391","https://openalex.org/W2106293441","https://openalex.org/W2137526645","https://openalex.org/W2140302584","https://openalex.org/W2141157874","https://openalex.org/W2146077306","https://openalex.org/W2156324925"],"related_works":["https://openalex.org/W3170299350","https://openalex.org/W2368410102","https://openalex.org/W2368037387","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"],"abstract_inverted_index":{"MOTIVATION":[0],"AND":[1],"RESULTS:":[2],"Motivated":[3],"by":[4,123],"the":[5,26,43,67,91,103,106,124,145],"recent":[6],"rise":[7],"of":[8,47],"interest":[9],"in":[10,29,69,96,102],"small":[11],"regulatory":[12],"RNAs,":[13],"we":[14],"present":[15],"Locomotif--a":[16],"new":[17],"approach":[18],"for":[19,109,142,148],"locating":[20],"RNA":[21,48,98],"motifs":[22,53,99],"that":[23],"goes":[24],"beyond":[25],"previous":[27],"ones":[28],"three":[30],"ways:":[31],"(1)":[32],"motif":[33],"search":[34,62],"is":[35,112,160],"based":[36],"on":[37,133,144],"efficient":[38],"dynamic":[39],"programming":[40],"algorithms,":[41],"incorporating":[42],"established":[44],"thermodynamic":[45],"model":[46],"secondary":[49,80],"structure":[50],"formation.":[51],"(2)":[52],"are":[54,64,100,121,129,138],"described":[55],"graphically,":[56],"using":[57],"a":[58,70,117,134],"Java-based":[59],"editor,":[60],"and":[61,85,131,147],"algorithms":[63],"derived":[65],"from":[66],"graphics":[68],"fully":[71],"automatic":[72],"way.":[73],"The":[74],"editor":[75],"allows":[76],"us":[77],"to":[78],"draw":[79],"structures,":[81],"annotated":[82],"with":[83],"size":[84],"sequence":[86],"information.":[87],"They":[88,137],"closely":[89],"resemble":[90],"established,":[92],"but":[93],"informal":[94],"way":[95],"which":[97],"communicated":[101],"literature.":[104],"Thus,":[105],"learning":[107],"effort":[108],"Locomotif":[110,115,159],"users":[111],"minimal.":[113],"(3)":[114],"employs":[116],"client-server":[118],"approach.":[119],"Motifs":[120],"designed":[122],"user":[125],"locally.":[126],"Search":[127],"programs":[128],"generated":[130],"compiled":[132],"bioinformatics":[135],"server.":[136],"made":[139],"available":[140,161],"both":[141],"execution":[143],"server,":[146],"download":[149],"as":[150],"C":[151],"source":[152],"code":[153],"plus":[154],"an":[155],"appropriate":[156],"makefile.":[157],"AVAILABILITY:":[158],"at":[162],"http://bibiserv.techfak.uni-bielefeld.de/locomotif.":[163]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":7},{"year":2013,"cited_by_count":5}],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2025-10-10T00:00:00"}
