{"id":"https://openalex.org/W2018144904","doi":"https://doi.org/10.1093/nar/gkg568","title":"A software tool-box for analysis of regulatory RNA elements","display_name":"A software tool-box for analysis of regulatory RNA elements","publication_year":2003,"publication_date":"2003-06-25","ids":{"openalex":"https://openalex.org/W2018144904","doi":"https://doi.org/10.1093/nar/gkg568","mag":"2018144904","pmid":"https://pubmed.ncbi.nlm.nih.gov/12824342"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkg568","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkg568","pdf_url":"https://academic.oup.com/nar/article-pdf/31/13/3441/9487376/gkg568.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":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":"Nucleic Acids Research","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/nar/article-pdf/31/13/3441/9487376/gkg568.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5059136056","display_name":"Peter Bengert","orcid":null},"institutions":[{"id":"https://openalex.org/I223822909","display_name":"Heidelberg University","ror":"https://ror.org/038t36y30","country_code":"DE","type":"education","lineage":["https://openalex.org/I223822909"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"P. Bengert","raw_affiliation_strings":["Parasitology, University of Heidelberg, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Parasitology, University of Heidelberg, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany","institution_ids":["https://openalex.org/I223822909"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5059136056"],"corresponding_institution_ids":["https://openalex.org/I223822909"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":null,"fwci":0.868,"has_fulltext":true,"cited_by_count":40,"citation_normalized_percentile":{"value":0.70122756,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"31","issue":"13","first_page":"3441","last_page":"3445"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":1.0,"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":1.0,"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":0.9998000264167786,"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":0.9994999766349792,"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/rna","display_name":"RNA","score":0.7672330141067505},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.7172343730926514},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6169182658195496},{"id":"https://openalex.org/keywords/nucleic-acid-structure","display_name":"Nucleic acid structure","score":0.5510054230690002},{"id":"https://openalex.org/keywords/rna-splicing","display_name":"RNA splicing","score":0.5505806803703308},{"id":"https://openalex.org/keywords/template","display_name":"Template","score":0.49345722794532776},{"id":"https://openalex.org/keywords/riboswitch","display_name":"Riboswitch","score":0.45668211579322815},{"id":"https://openalex.org/keywords/intron","display_name":"Intron","score":0.4356445372104645},{"id":"https://openalex.org/keywords/non-coding-rna","display_name":"Non-coding RNA","score":0.39725133776664734},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3897193670272827},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.2386283278465271},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.20978853106498718},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.07799580693244934}],"concepts":[{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.7672330141067505},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.7172343730926514},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6169182658195496},{"id":"https://openalex.org/C126142528","wikidata":"https://www.wikidata.org/wiki/Q3771876","display_name":"Nucleic acid structure","level":4,"score":0.5510054230690002},{"id":"https://openalex.org/C54458228","wikidata":"https://www.wikidata.org/wiki/Q237218","display_name":"RNA splicing","level":4,"score":0.5505806803703308},{"id":"https://openalex.org/C82714645","wikidata":"https://www.wikidata.org/wiki/Q438331","display_name":"Template","level":2,"score":0.49345722794532776},{"id":"https://openalex.org/C148625055","wikidata":"https://www.wikidata.org/wiki/Q418840","display_name":"Riboswitch","level":5,"score":0.45668211579322815},{"id":"https://openalex.org/C94671646","wikidata":"https://www.wikidata.org/wiki/Q207551","display_name":"Intron","level":3,"score":0.4356445372104645},{"id":"https://openalex.org/C194993378","wikidata":"https://www.wikidata.org/wiki/Q427087","display_name":"Non-coding RNA","level":4,"score":0.39725133776664734},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3897193670272827},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.2386283278465271},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.20978853106498718},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.07799580693244934}],"mesh":[{"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":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","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":"D016337","descriptor_name":"RNA, Catalytic","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D016337","descriptor_name":"RNA, Catalytic","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D016337","descriptor_name":"RNA, Catalytic","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"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":"D038621","descriptor_name":"Regulatory Sequences, Ribonucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D038621","descriptor_name":"Regulatory Sequences, Ribonucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D038621","descriptor_name":"Regulatory Sequences, Ribonucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":6,"locations":[{"id":"doi:10.1093/nar/gkg568","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkg568","pdf_url":"https://academic.oup.com/nar/article-pdf/31/13/3441/9487376/gkg568.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":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":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:12824342","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/12824342","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":null},{"id":"pmh:oai:edoc.mdc-berlin.de:6716","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4306400224","display_name":"MDC Repository (Max-Delbrueck-Center for Molecular Medicine)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I149899117","host_organization_name":"Max Planck Society","host_organization_lineage":["https://openalex.org/I149899117"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"","raw_type":"Article"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.819.6666","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.819.6666","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"https://nar.oxfordjournals.org/content/31/13/3441.full.pdf","raw_type":"text"},{"id":"pmh:oai:europepmc.org:158836","is_oa":false,"landing_page_url":"http://europepmc.org/pmc/articles/PMC168974","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":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:168974","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/168974","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":"Nucleic Acids Res","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/nar/gkg568","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkg568","pdf_url":"https://academic.oup.com/nar/article-pdf/31/13/3441/9487376/gkg568.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":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":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.7699999809265137,"id":"https://metadata.un.org/sdg/7","display_name":"Affordable and clean energy"}],"awards":[{"id":"https://openalex.org/G3317018093","display_name":null,"funder_award_id":"SFB 544/B2","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G5216269092","display_name":null,"funder_award_id":"SFB544","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"}],"funders":[{"id":"https://openalex.org/F4320320879","display_name":"Deutsche Forschungsgemeinschaft","ror":"https://ror.org/018mejw64"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2018144904.pdf","grobid_xml":"https://content.openalex.org/works/W2018144904.grobid-xml"},"referenced_works_count":20,"referenced_works":["https://openalex.org/W165213868","https://openalex.org/W299581075","https://openalex.org/W382720467","https://openalex.org/W1543796220","https://openalex.org/W1996789245","https://openalex.org/W2002508855","https://openalex.org/W2019328719","https://openalex.org/W2030255811","https://openalex.org/W2036456126","https://openalex.org/W2037535999","https://openalex.org/W2064345118","https://openalex.org/W2082971144","https://openalex.org/W2084875499","https://openalex.org/W2093543202","https://openalex.org/W2142056356","https://openalex.org/W2149429041","https://openalex.org/W2151831732","https://openalex.org/W2166187656","https://openalex.org/W4236630749","https://openalex.org/W4250052351"],"related_works":["https://openalex.org/W1507571087","https://openalex.org/W2756374846","https://openalex.org/W2083416401","https://openalex.org/W3170509043","https://openalex.org/W2116507553","https://openalex.org/W2922047510","https://openalex.org/W1965032074","https://openalex.org/W2274017406","https://openalex.org/W2951664338","https://openalex.org/W2805826204"],"abstract_inverted_index":{"We":[0],"describe":[1],"an":[2,39,78],"integrated":[3],"tool-box":[4],"to":[5,76,100,128,135],"identify":[6],"regulatory":[7],"RNA":[8,11,21,40,53,74,82,115,121],"elements.":[9],"The":[10,138],"analyzer":[12],"collects":[13],"general":[14],"and":[15,32,49,91],"specific":[16,52],"information":[17],"on":[18],"any":[19,105],"submitted":[20],"sequence":[22],"or":[23,119],"batch":[24],"of":[25,38,57,80],"sequences":[26],"in":[27,47,66],"FASTA":[28],"format.":[29],"It":[30,69],"determines":[31],"rapidly":[33],"scans":[34],"the":[35,81,131],"different":[36],"regions":[37],"(including":[41],"5'":[42],"UTR,":[43],"CDS,":[44],"3'":[45,67],"UTR":[46],"mRNA)":[48],"screens":[50],"for":[51,109],"signals":[54],"(in":[55],"each":[56],"these":[58,136],"regions,":[59],"e.g.":[60],"polyA-site,":[61],"AU":[62],"rich":[63],"region":[64],"etc.":[65],"UTR).":[68],"runs":[70],"a":[71,145],"fast":[72],"folding":[73],"routine":[75],"provide":[77],"overview":[79],"fold.":[83],"Furthermore":[84],"it":[85],"analyzes":[86],"structure":[87],"content,":[88],"fold":[89],"energy":[90],"stem":[92],"loops.":[93],"In":[94],"addition,":[95],"consensus":[96],"templates":[97],"are":[98,104],"used":[99],"determine":[101],"whether":[102],"there":[103],"functional":[106],"structures":[107,132],"present":[108],"translational":[110],"control":[111],"(template:":[112,116,122],"IRE),":[113],"structured":[114],"tRNA":[117],"consensus)":[118],"catalytic":[120],"trans-splicing":[123],"RNA),":[124],"giving":[125],"indications":[126],"as":[127,144],"how":[129],"well":[130],"found":[133],"match":[134],"templates.":[137],"tool":[139],"box":[140],"has":[141],"been":[142],"implemented":[143],"WWW":[146],"server":[147],"at":[148],"http://wb2x01.biozentrum.uni-wuerzburg.de/.":[149]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":1},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":4}],"updated_date":"2026-08-01T09:00:35.917206","created_date":"2025-10-10T00:00:00"}
