{"id":"https://openalex.org/W2150882562","doi":"https://doi.org/10.1093/bioinformatics/btn544","title":"IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions","display_name":"IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions","publication_year":2008,"publication_date":"2008-10-21","ids":{"openalex":"https://openalex.org/W2150882562","doi":"https://doi.org/10.1093/bioinformatics/btn544","mag":"2150882562","pmid":"https://pubmed.ncbi.nlm.nih.gov/18940824"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btn544","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btn544","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/24/24/2849/49056366/bioinformatics_24_24_2849.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/24/24/2849/49056366/bioinformatics_24_24_2849.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5031748489","display_name":"Anke Busch","orcid":"https://orcid.org/0000-0002-2232-1329"},"institutions":[{"id":"https://openalex.org/I161046081","display_name":"University of Freiburg","ror":"https://ror.org/0245cg223","country_code":"DE","type":"education","lineage":["https://openalex.org/I161046081"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Anke Busch","raw_affiliation_strings":["Bioinformatics Group, Albert-Ludwigs-University Freiburg, Georges-Koehler-Allee 106, Freiburg D-79110, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics Group, Albert-Ludwigs-University Freiburg, Georges-Koehler-Allee 106, Freiburg D-79110, Germany","institution_ids":["https://openalex.org/I161046081"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079662525","display_name":"Andreas S. Richter","orcid":"https://orcid.org/0000-0002-4166-0991"},"institutions":[{"id":"https://openalex.org/I161046081","display_name":"University of Freiburg","ror":"https://ror.org/0245cg223","country_code":"DE","type":"education","lineage":["https://openalex.org/I161046081"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Andreas S. Richter","raw_affiliation_strings":["Bioinformatics Group, Albert-Ludwigs-University Freiburg, Georges-Koehler-Allee 106, Freiburg D-79110, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics Group, Albert-Ludwigs-University Freiburg, Georges-Koehler-Allee 106, Freiburg D-79110, Germany","institution_ids":["https://openalex.org/I161046081"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5017672883","display_name":"Rolf Backofen","orcid":"https://orcid.org/0000-0001-8231-3323"},"institutions":[{"id":"https://openalex.org/I161046081","display_name":"University of Freiburg","ror":"https://ror.org/0245cg223","country_code":"DE","type":"education","lineage":["https://openalex.org/I161046081"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Rolf Backofen","raw_affiliation_strings":["Bioinformatics Group, Albert-Ludwigs-University Freiburg, Georges-Koehler-Allee 106, Freiburg D-79110, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics Group, Albert-Ludwigs-University Freiburg, Georges-Koehler-Allee 106, Freiburg D-79110, Germany","institution_ids":["https://openalex.org/I161046081"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5017672883"],"corresponding_institution_ids":["https://openalex.org/I161046081"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":10.5815,"has_fulltext":true,"cited_by_count":561,"citation_normalized_percentile":{"value":0.98611111,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"24","issue":"24","first_page":"2849","last_page":"2856"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10120","display_name":"Bacterial Genetics and Biotechnology","score":0.9322999715805054,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T10120","display_name":"Bacterial Genetics and Biotechnology","score":0.9322999715805054,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.039500001817941666,"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":0.019500000402331352,"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/transfer-rna","display_name":"Transfer RNA","score":0.6159777045249939},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6135420799255371},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.5395421981811523},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.48588699102401733},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.47591596841812134},{"id":"https://openalex.org/keywords/bacterial-genome-size","display_name":"Bacterial genome size","score":0.47200891375541687},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.4556047320365906},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.37028321623802185},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1834213137626648}],"concepts":[{"id":"https://openalex.org/C153957851","wikidata":"https://www.wikidata.org/wiki/Q201448","display_name":"Transfer RNA","level":4,"score":0.6159777045249939},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6135420799255371},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.5395421981811523},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.48588699102401733},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.47591596841812134},{"id":"https://openalex.org/C3742359","wikidata":"https://www.wikidata.org/wiki/Q4839988","display_name":"Bacterial genome size","level":4,"score":0.47200891375541687},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.4556047320365906},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.37028321623802185},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1834213137626648}],"mesh":[{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012329","descriptor_name":"RNA, Bacterial","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012329","descriptor_name":"RNA, Bacterial","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012329","descriptor_name":"RNA, Bacterial","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":"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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D022661","descriptor_name":"RNA, Untranslated","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D022661","descriptor_name":"RNA, Untranslated","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D022661","descriptor_name":"RNA, Untranslated","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btn544","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btn544","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/24/24/2849/49056366/bioinformatics_24_24_2849.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:18940824","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/18940824","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":null},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.568.977","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.568.977","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://bioinformatics.oxfordjournals.org/content/early/2008/10/21/bioinformatics.btn544.full.pdf","raw_type":"text"},{"id":"pmh:oai:pubmedcentral.nih.gov:2639303","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2639303","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"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btn544","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btn544","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/24/24/2849/49056366/bioinformatics_24_24_2849.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":[{"id":"https://openalex.org/G1263940194","display_name":null,"funder_award_id":"SPP 1258","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G2386046523","display_name":null,"funder_award_id":"BA 2168/2-1 SPP 1258","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G894356745","display_name":null,"funder_award_id":"0313921","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"}],"funders":[{"id":"https://openalex.org/F4320320879","display_name":"Deutsche Forschungsgemeinschaft","ror":"https://ror.org/018mejw64"},{"id":"https://openalex.org/F4320321114","display_name":"Bundesministerium f\u00fcr Bildung und Forschung","ror":"https://ror.org/04pz7b180"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2150882562.pdf","grobid_xml":"https://content.openalex.org/works/W2150882562.grobid-xml"},"referenced_works_count":62,"referenced_works":["https://openalex.org/W30210889","https://openalex.org/W144423133","https://openalex.org/W1543796220","https://openalex.org/W1587079335","https://openalex.org/W1934866768","https://openalex.org/W1969445034","https://openalex.org/W1975148447","https://openalex.org/W1977298702","https://openalex.org/W1983815263","https://openalex.org/W1984675364","https://openalex.org/W1992102098","https://openalex.org/W1993799748","https://openalex.org/W1998137451","https://openalex.org/W1999530403","https://openalex.org/W2002013652","https://openalex.org/W2007501617","https://openalex.org/W2008593438","https://openalex.org/W2009326616","https://openalex.org/W2009818318","https://openalex.org/W2011879414","https://openalex.org/W2019381697","https://openalex.org/W2022916085","https://openalex.org/W2025763720","https://openalex.org/W2026856977","https://openalex.org/W2028102516","https://openalex.org/W2030120875","https://openalex.org/W2033677231","https://openalex.org/W2037297533","https://openalex.org/W2043653977","https://openalex.org/W2054260432","https://openalex.org/W2073865971","https://openalex.org/W2078260514","https://openalex.org/W2088784401","https://openalex.org/W2088930981","https://openalex.org/W2088998577","https://openalex.org/W2089450351","https://openalex.org/W2094253263","https://openalex.org/W2099915551","https://openalex.org/W2101856858","https://openalex.org/W2102017611","https://openalex.org/W2109136664","https://openalex.org/W2119336718","https://openalex.org/W2122771148","https://openalex.org/W2126732736","https://openalex.org/W2129706781","https://openalex.org/W2134653938","https://openalex.org/W2136361016","https://openalex.org/W2136659582","https://openalex.org/W2139271133","https://openalex.org/W2141543393","https://openalex.org/W2149785901","https://openalex.org/W2151994495","https://openalex.org/W2153276014","https://openalex.org/W2154085311","https://openalex.org/W2155318580","https://openalex.org/W2159850373","https://openalex.org/W2161159766","https://openalex.org/W2164700062","https://openalex.org/W4211039187","https://openalex.org/W4240231372","https://openalex.org/W4285719527","https://openalex.org/W6684319383"],"related_works":["https://openalex.org/W2079327011","https://openalex.org/W2889029343","https://openalex.org/W2056973287","https://openalex.org/W2061340009","https://openalex.org/W3111025641","https://openalex.org/W3202542829","https://openalex.org/W1965562485","https://openalex.org/W2340204314","https://openalex.org/W1956137100","https://openalex.org/W2104081677"],"abstract_inverted_index":{"MOTIVATION:":[0],"During":[1],"the":[2,46,69,75,108,121,132,140,144],"last":[3],"few":[4],"years,":[5],"several":[6],"new":[7,102],"small":[8],"regulatory":[9],"RNAs":[10,90],"(sRNAs)":[11],"have":[12,41],"been":[13,43],"discovered":[14],"in":[15,60],"bacteria.":[16],"Most":[17],"of":[18,48,71,77,89,110,115,123,134,143],"them":[19],"act":[20],"as":[21,118,120],"post-transcriptional":[22],"regulators":[23],"by":[24],"base":[25],"pairing":[26],"to":[27,86,107,131],"a":[28,78,101,124,147],"target":[29,57,65,72,116],"mRNA,":[30],"causing":[31],"translational":[32],"repression":[33],"or":[34,36,91],"activation,":[35],"mRNA":[37],"degradation.":[38],"Numerous":[39],"sRNAs":[40],"already":[42],"identified,":[44],"but":[45],"number":[47],"experimentally":[49],"verified":[50],"targets":[51,137],"is":[52,59],"considerably":[53],"lower.":[54],"Consequently,":[55],"computational":[56],"prediction":[58,66,109,133],"great":[61],"demand.":[62],"Many":[63],"existing":[64],"programs":[67],"neglect":[68],"accessibility":[70,114],"sites":[73,117],"and":[74,104,138],"existence":[76,122],"seed,":[79],"while":[80],"other":[81],"approaches":[82],"are":[83],"either":[84],"specialized":[85],"certain":[87],"types":[88],"too":[92],"slow":[93],"for":[94],"genome-wide":[95],"searches.":[96],"RESULTS:":[97],"We":[98,127],"introduce":[99],"INTARNA,":[100],"general":[103],"fast":[105],"approach":[106],"RNA-RNA":[111],"interactions":[112,145],"incorporating":[113],"well":[119],"user-definable":[125],"seed.":[126],"successfully":[128],"applied":[129],"INTARNA":[130],"bacterial":[135],"sRNA":[136],"determined":[139],"exact":[141],"locations":[142],"with":[146],"higher":[148],"accuracy":[149],"than":[150],"competing":[151],"programs.":[152],"AVAILABILITY:":[153],"http://www.bioinf.uni-freiburg.de/Software/":[154]},"counts_by_year":[{"year":2026,"cited_by_count":13},{"year":2025,"cited_by_count":34},{"year":2024,"cited_by_count":24},{"year":2023,"cited_by_count":38},{"year":2022,"cited_by_count":41},{"year":2021,"cited_by_count":33},{"year":2020,"cited_by_count":33},{"year":2019,"cited_by_count":43},{"year":2018,"cited_by_count":54},{"year":2017,"cited_by_count":42},{"year":2016,"cited_by_count":42},{"year":2015,"cited_by_count":23},{"year":2014,"cited_by_count":30},{"year":2013,"cited_by_count":20},{"year":2012,"cited_by_count":36}],"updated_date":"2026-06-23T06:36:01.041984","created_date":"2025-10-10T00:00:00"}
