{"id":"https://openalex.org/W2931564089","doi":"https://doi.org/10.1186/s12859-019-2704-x","title":"RhoTermPredict: an algorithm for predicting Rho-dependent transcription terminators based on Escherichia coli, Bacillus subtilis and Salmonella enterica databases","display_name":"RhoTermPredict: an algorithm for predicting Rho-dependent transcription terminators based on Escherichia coli, Bacillus subtilis and Salmonella enterica databases","publication_year":2019,"publication_date":"2019-03-07","ids":{"openalex":"https://openalex.org/W2931564089","doi":"https://doi.org/10.1186/s12859-019-2704-x","mag":"2931564089","pmid":"https://pubmed.ncbi.nlm.nih.gov/30845912"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-019-2704-x","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-2704-x","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-019-2704-x","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-019-2704-x","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5106135680","display_name":"Marco Di Salvo","orcid":null},"institutions":[{"id":"https://openalex.org/I142910587","display_name":"University of Salento","ror":"https://ror.org/03fc1k060","country_code":"IT","type":"education","lineage":["https://openalex.org/I142910587"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Marco Di Salvo","raw_affiliation_strings":["Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy","Dipartimento di Scienze e Technologie Biologiche ed Ambientali [Lecce] (Piazza Tancredi, n7 - 73100 Lecce - Italy)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy","institution_ids":["https://openalex.org/I142910587"]},{"raw_affiliation_string":"Dipartimento di Scienze e Technologie Biologiche ed Ambientali [Lecce] (Piazza Tancredi, n7 - 73100 Lecce - Italy)","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081525912","display_name":"Simone Puccio","orcid":"https://orcid.org/0000-0003-4007-4365"},"institutions":[{"id":"https://openalex.org/I1339471597","display_name":"Humanitas University","ror":"https://ror.org/020dggs04","country_code":"IT","type":"education","lineage":["https://openalex.org/I1339471597"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Simone Puccio","raw_affiliation_strings":["Humanitas Clinical and Research Center, Rozzano, Milan, Italy","Humanitas Clinical and Research Center [Rozzano, Milan, Italy] (Via Manzoni, 56 Rozzano, 20089. - Italy)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Humanitas Clinical and Research Center, Rozzano, Milan, Italy","institution_ids":["https://openalex.org/I1339471597"]},{"raw_affiliation_string":"Humanitas Clinical and Research Center [Rozzano, Milan, Italy] (Via Manzoni, 56 Rozzano, 20089. - Italy)","institution_ids":["https://openalex.org/I1339471597"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076496892","display_name":"Clelia Peano","orcid":"https://orcid.org/0000-0001-7055-3629"},"institutions":[{"id":"https://openalex.org/I1339471597","display_name":"Humanitas University","ror":"https://ror.org/020dggs04","country_code":"IT","type":"education","lineage":["https://openalex.org/I1339471597"]},{"id":"https://openalex.org/I4210154278","display_name":"Institute of Biomedical Technologies","ror":"https://ror.org/04ehykb85","country_code":"IT","type":"facility","lineage":["https://openalex.org/I4210154278","https://openalex.org/I4210155236"]},{"id":"https://openalex.org/I4210155236","display_name":"National Research Council","ror":"https://ror.org/04zaypm56","country_code":"IT","type":"nonprofit","lineage":["https://openalex.org/I4210155236"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Clelia Peano","raw_affiliation_strings":["Humanitas Clinical and Research Center, Rozzano, Milan, Italy","Institute of Genetics and Biomedical Research UoS of Milan, National Research Council, Rozzano, Milan, Italy","ITB - Istituto di Tecnologie Biomediche [Segrate] (Via Fratelli Cervi, 93 20090 Segrate (MI) - Italy)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Humanitas Clinical and Research Center, Rozzano, Milan, Italy","institution_ids":["https://openalex.org/I1339471597"]},{"raw_affiliation_string":"Institute of Genetics and Biomedical Research UoS of Milan, National Research Council, Rozzano, Milan, Italy","institution_ids":["https://openalex.org/I4210155236"]},{"raw_affiliation_string":"ITB - Istituto di Tecnologie Biomediche [Segrate] (Via Fratelli Cervi, 93 20090 Segrate (MI) - Italy)","institution_ids":["https://openalex.org/I4210154278"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039330974","display_name":"St\u00e9phan Lacour","orcid":"https://orcid.org/0000-0002-6066-4189"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I4210101348","display_name":"Centre Inria de l'Universit\u00e9 Grenoble Alpes","ror":"https://ror.org/00n8d6z93","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1326498283","https://openalex.org/I4210101348"]},{"id":"https://openalex.org/I4210113150","display_name":"Laboratoire Interdisciplinaire de Physique","ror":"https://ror.org/023n9q531","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I4210113150","https://openalex.org/I899635006"]},{"id":"https://openalex.org/I899635006","display_name":"Universit\u00e9 Grenoble Alpes","ror":"https://ror.org/02rx3b187","country_code":"FR","type":"education","lineage":["https://openalex.org/I899635006"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Stephan Lacour","raw_affiliation_strings":["Univ. Grenoble Alpes, CNRS, Inria, LIPhy (UMR5588), 38000, Grenoble, France","LIPhy - Laboratoire Interdisciplinaire de Physique [Saint Martin d\u2019H\u00e8res] (140 rue de la Physique\r\n38058 Grenoble cedex 9 - France)","IBIS - Modeling, simulation, measurement, and control of bacterial regulatory networks (655 avenue de l'Europe, Montbonnot, 38334 Saint Ismier CEDEX, France - France)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Univ. Grenoble Alpes, CNRS, Inria, LIPhy (UMR5588), 38000, Grenoble, France","institution_ids":["https://openalex.org/I4210113150","https://openalex.org/I4210101348","https://openalex.org/I1294671590","https://openalex.org/I899635006"]},{"raw_affiliation_string":"LIPhy - Laboratoire Interdisciplinaire de Physique [Saint Martin d\u2019H\u00e8res] (140 rue de la Physique\r\n38058 Grenoble cedex 9 - France)","institution_ids":["https://openalex.org/I4210113150"]},{"raw_affiliation_string":"IBIS - Modeling, simulation, measurement, and control of bacterial regulatory networks (655 avenue de l'Europe, Montbonnot, 38334 Saint Ismier CEDEX, France - France)","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5050802580","display_name":"Pietro Alifano","orcid":"https://orcid.org/0000-0003-3768-7275"},"institutions":[{"id":"https://openalex.org/I142910587","display_name":"University of Salento","ror":"https://ror.org/03fc1k060","country_code":"IT","type":"education","lineage":["https://openalex.org/I142910587"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Pietro Alifano","raw_affiliation_strings":["Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy. pietro.alifano@unisalento.it","Dipartimento di Scienze e Technologie Biologiche ed Ambientali [Lecce] (Piazza Tancredi, n7 - 73100 Lecce - Italy)"],"raw_orcid":"https://orcid.org/0000-0003-3768-7275","affiliations":[{"raw_affiliation_string":"Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy. pietro.alifano@unisalento.it","institution_ids":["https://openalex.org/I142910587"]},{"raw_affiliation_string":"Dipartimento di Scienze e Technologie Biologiche ed Ambientali [Lecce] (Piazza Tancredi, n7 - 73100 Lecce - Italy)","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5050802580"],"corresponding_institution_ids":["https://openalex.org/I142910587"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":2.137,"has_fulltext":true,"cited_by_count":62,"citation_normalized_percentile":{"value":0.87973421,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"20","issue":"1","first_page":"117","last_page":"117"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.3930000066757202,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.3930000066757202,"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/T10120","display_name":"Bacterial Genetics and Biotechnology","score":0.3626999855041504,"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":0.1868000030517578,"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/salmonella-enterica","display_name":"Salmonella enterica","score":0.7283729910850525},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.7156303524971008},{"id":"https://openalex.org/keywords/rna-polymerase","display_name":"RNA polymerase","score":0.6066559553146362},{"id":"https://openalex.org/keywords/bacillus-subtilis","display_name":"Bacillus subtilis","score":0.5928440690040588},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.5836571455001831},{"id":"https://openalex.org/keywords/transcription","display_name":"Transcription (linguistics)","score":0.5475656390190125},{"id":"https://openalex.org/keywords/escherichia-coli","display_name":"Escherichia coli","score":0.5311720967292786},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.525894820690155},{"id":"https://openalex.org/keywords/bacterial-genome-size","display_name":"Bacterial genome size","score":0.49701979756355286},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4608144164085388},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.41229236125946045},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.41103699803352356},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.26712876558303833},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.19662714004516602},{"id":"https://openalex.org/keywords/bacteria","display_name":"Bacteria","score":0.10749435424804688}],"concepts":[{"id":"https://openalex.org/C2779607309","wikidata":"https://www.wikidata.org/wiki/Q2264864","display_name":"Salmonella enterica","level":4,"score":0.7283729910850525},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.7156303524971008},{"id":"https://openalex.org/C2776449523","wikidata":"https://www.wikidata.org/wiki/Q272631","display_name":"RNA polymerase","level":4,"score":0.6066559553146362},{"id":"https://openalex.org/C2777272437","wikidata":"https://www.wikidata.org/wiki/Q131238","display_name":"Bacillus subtilis","level":3,"score":0.5928440690040588},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5836571455001831},{"id":"https://openalex.org/C179926584","wikidata":"https://www.wikidata.org/wiki/Q207714","display_name":"Transcription (linguistics)","level":2,"score":0.5475656390190125},{"id":"https://openalex.org/C547475151","wikidata":"https://www.wikidata.org/wiki/Q25419","display_name":"Escherichia coli","level":3,"score":0.5311720967292786},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.525894820690155},{"id":"https://openalex.org/C3742359","wikidata":"https://www.wikidata.org/wiki/Q4839988","display_name":"Bacterial genome size","level":4,"score":0.49701979756355286},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4608144164085388},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.41229236125946045},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.41103699803352356},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.26712876558303833},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.19662714004516602},{"id":"https://openalex.org/C523546767","wikidata":"https://www.wikidata.org/wiki/Q10876","display_name":"Bacteria","level":2,"score":0.10749435424804688},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"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":"D001412","descriptor_name":"Bacillus subtilis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001412","descriptor_name":"Bacillus subtilis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001412","descriptor_name":"Bacillus subtilis","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"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":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012234","descriptor_name":"Rho Factor","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012234","descriptor_name":"Rho Factor","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012234","descriptor_name":"Rho Factor","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012329","descriptor_name":"RNA, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012329","descriptor_name":"RNA, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012329","descriptor_name":"RNA, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013728","descriptor_name":"Terminator Regions, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013728","descriptor_name":"Terminator Regions, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013728","descriptor_name":"Terminator Regions, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","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":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019779","descriptor_name":"Salmonella enterica","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D019779","descriptor_name":"Salmonella enterica","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D019779","descriptor_name":"Salmonella enterica","qualifier_ui":"Q000235","qualifier_name":"genetics","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},{"descriptor_ui":"D048168","descriptor_name":"Escherichia coli K12","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D048168","descriptor_name":"Escherichia coli K12","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D048168","descriptor_name":"Escherichia coli K12","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1186/s12859-019-2704-x","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-2704-x","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-019-2704-x","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:30845912","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30845912","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:6407284","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6407284","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:HAL:hal-02423208v1","is_oa":true,"landing_page_url":"https://inria.hal.science/hal-02423208","pdf_url":null,"source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, 2019, 20 (1), pp.1-11. &#x27E8;10.1186/s12859-019-2704-x&#x27E9;","raw_type":"Journal articles"},{"id":"pmh:oai:doaj.org/article:e5074a4a59b54a8294449450f88caae0","is_oa":true,"landing_page_url":"https://doaj.org/article/e5074a4a59b54a8294449450f88caae0","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 20, Iss 1, Pp 1-11 (2019)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:5409817","is_oa":true,"landing_page_url":"http://europepmc.org/pmc/articles/PMC6407284","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-019-2704-x","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-2704-x","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-019-2704-x","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3781278721","display_name":null,"funder_award_id":"PON01_02093","funder_id":"https://openalex.org/F4320321873","funder_display_name":"Ministero dell\u2019Istruzione, dell\u2019Universit\u00e0 e della Ricerca"}],"funders":[{"id":"https://openalex.org/F4320321873","display_name":"Ministero dell\u2019Istruzione, dell\u2019Universit\u00e0 e della Ricerca","ror":"https://ror.org/0166hxq48"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2931564089.pdf","grobid_xml":"https://content.openalex.org/works/W2931564089.grobid-xml"},"referenced_works_count":42,"referenced_works":["https://openalex.org/W638577851","https://openalex.org/W1498446020","https://openalex.org/W1508972499","https://openalex.org/W1559990160","https://openalex.org/W1602283030","https://openalex.org/W1968138552","https://openalex.org/W1976765586","https://openalex.org/W1986778616","https://openalex.org/W1993371345","https://openalex.org/W1998666298","https://openalex.org/W2005436483","https://openalex.org/W2007697111","https://openalex.org/W2012681204","https://openalex.org/W2013115542","https://openalex.org/W2013602190","https://openalex.org/W2041032992","https://openalex.org/W2042070371","https://openalex.org/W2050868944","https://openalex.org/W2066180705","https://openalex.org/W2077460182","https://openalex.org/W2077777080","https://openalex.org/W2092792860","https://openalex.org/W2094967416","https://openalex.org/W2109295007","https://openalex.org/W2117242887","https://openalex.org/W2134153749","https://openalex.org/W2136067498","https://openalex.org/W2142706774","https://openalex.org/W2152954697","https://openalex.org/W2156274103","https://openalex.org/W2160529079","https://openalex.org/W2170839158","https://openalex.org/W2199968103","https://openalex.org/W2287897768","https://openalex.org/W2322749552","https://openalex.org/W2442768485","https://openalex.org/W2599413193","https://openalex.org/W2604456776","https://openalex.org/W2738840941","https://openalex.org/W2787044201","https://openalex.org/W2797492921","https://openalex.org/W2809185198"],"related_works":["https://openalex.org/W4293061103","https://openalex.org/W3041516390","https://openalex.org/W1548672655","https://openalex.org/W3025683560","https://openalex.org/W2301778769","https://openalex.org/W4238511776","https://openalex.org/W2359352982","https://openalex.org/W2758340467","https://openalex.org/W2354946010","https://openalex.org/W2162450681"],"abstract_inverted_index":{"In":[0,49,134],"bacterial":[1,151,347],"genomes,":[2],"there":[3],"are":[4,23,113],"two":[5],"mechanisms":[6],"to":[7,39,63,82,165,340],"terminate":[8],"the":[9,12,18,44,56,79,90,104,109,120,140,200,215,226,244,247,255,288,312,343],"DNA":[10],"transcription:":[11],"\u201cintrinsic\u201d":[13],"or":[14],"Rho-independent":[15],"termination":[16,52],"and":[17,76,115,187,211,224,228,236,251,282,316],"Rho-dependent":[19,51,94,130,147,167,308],"termination.":[20],"Intrinsic":[21],"terminators":[22,95,131,148,259,309,336,345],"characterized":[24,69,180],"by":[25,30,55,70,181,194,207,254],"a":[26,31,67,71,99,159,174,182,195,268,284,304],"RNA":[27,80,201],"hairpin":[28],"followed":[29,193],"run":[32],"of":[33,43,93,111,214,249,257,290],"6\u20138":[34],"U":[35],"residues":[36],"relatively":[37],"easy":[38],"identify":[40],"using":[41,208],"one":[42],"numerous":[45],"available":[46,209,229],"prediction":[47,92,132,149],"programs.":[48],"contrast,":[50],"is":[53,98,119,267,303],"mediated":[54],"Rho":[57,112],"protein":[58],"factor":[59],"that,":[60],"firstly,":[61],"binds":[62],"ribosome-free":[64],"mRNA":[65],"in":[66,96,150,221,225,311,321,331,338,346],"site":[68,179,198],"C":[72,183,191],">":[73,184],"G":[74,185],"content":[75,186],"then":[77],"reaches":[78],"polymerase":[81],"induce":[83],"its":[84],"release.":[85],"Conversely":[86],"on":[87,158],"intrinsic":[88,258,335],"terminators,":[89],"computational":[91,322],"prokaryotes":[97],"very":[100,269,296],"difficult":[101],"problem":[102],"because":[103],"sequence":[105],"features":[106],"required":[107],"for":[108,144,173,199,273,283,307],"function":[110],"complex":[114],"poorly":[116],"defined.":[117],"This":[118],"reason":[121],"why":[122],"it":[123],"still":[124],"does":[125],"not":[126],"exist":[127],"an":[128,145,334],"exhaustive":[129,146],"program.":[133],"this":[135,319],"study":[136],"we":[137],"introduce":[138],"RhoTermPredict,":[139],"first":[141],"published":[142],"algorithm":[143,271],"genomes.":[152,240,348],"RhoTermPredict":[153,205,250,266,302,327],"identifies":[154],"these":[155],"elements":[156],"based":[157],"previously":[160],"proposed":[161],"consensus":[162],"motif":[163],"common":[164],"all":[166,342],"transcription":[168,344],"terminators.":[169],"It":[170],"essentially":[171],"searches":[172],"78":[175],"nt":[176],"long":[177],"RUT":[178],"with":[188,292,333],"regularly":[189],"spaced":[190],"residues,":[192],"putative":[196],"pause":[197],"polymerase.":[202],"We":[203,241,324],"tested":[204],"performances":[206],"genomic":[210,230],"transcriptomic":[212],"data":[213],"microorganism":[216],"Escherichia":[217],"coli":[218],"K-12,":[219],"both":[220,272],"limited-length":[222,274],"sequences":[223,231,275],"whole-genome,":[227],"from":[232],"Bacillus":[233],"subtilis":[234],"168":[235],"Salmonella":[237],"enterica":[238],"LT2":[239],"also":[242],"estimated":[243],"overlap":[245,291],"between":[246],"predictions":[248,294],"those":[252],"obtained":[253,279],"predictor":[256,337],"ARNold":[260,293],"webtool.":[261],"Our":[262,298],"results":[263],"demonstrated":[264],"that":[265,301,326],"performing":[270],"(F":[276],"1":[277],"-score":[278],"about":[280],"0.7)":[281],"genome-wide":[285],"analysis.":[286],"Furthermore":[287],"degree":[289],"was":[295],"low.":[297],"analysis":[299],"shows":[300],"powerful":[305],"tool":[306],"search":[310],"three":[313],"analyzed":[314],"genomes":[315],"could":[317,328],"fill":[318],"gap":[320],"genomics.":[323],"conclude":[325],"be":[329],"used":[330],"combination":[332],"order":[339],"predict":[341]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":11},{"year":2024,"cited_by_count":14},{"year":2023,"cited_by_count":8},{"year":2022,"cited_by_count":7},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":14},{"year":2019,"cited_by_count":2}],"updated_date":"2026-06-19T15:47:20.252518","created_date":"2025-10-10T00:00:00"}
