{"id":"https://openalex.org/W2043192186","doi":"https://doi.org/10.1186/1471-2105-8-464","title":"Predicting RNA secondary structure by the comparative approach: how to select the homologous sequences","display_name":"Predicting RNA secondary structure by the comparative approach: how to select the homologous sequences","publication_year":2007,"publication_date":"2007-11-28","ids":{"openalex":"https://openalex.org/W2043192186","doi":"https://doi.org/10.1186/1471-2105-8-464","mag":"2043192186","pmid":"https://pubmed.ncbi.nlm.nih.gov/18045491"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-8-464","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-8-464","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-8-464","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/10.1186/1471-2105-8-464","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5002907739","display_name":"St\u00e9fan Engelen","orcid":"https://orcid.org/0000-0003-0003-1192"},"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/I88467170","display_name":"Universit\u00e9 d'\u00c9vry Val-d'Essonne","ror":"https://ror.org/00e96v939","country_code":"FR","type":"education","lineage":["https://openalex.org/I277688954","https://openalex.org/I88467170"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"St\u00e9fan Engelen","raw_affiliation_strings":["Laboratoire IBISC - FRE CNRS 2873, CNRS, Universit\u00e9 d'Evry Val-d'Essonne, Genopole, 523, place des Terrasses, 91000 Evry, France. stefan.engelen@ibisc.univ-evry.fr","Laboratoire IBISC \u2013 FRE CNRS 2873. CNRS, Universit\u00e9 d'Evry Val-d'Essonne, Evry, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratoire IBISC - FRE CNRS 2873, CNRS, Universit\u00e9 d'Evry Val-d'Essonne, Genopole, 523, place des Terrasses, 91000 Evry, France. stefan.engelen@ibisc.univ-evry.fr","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I88467170"]},{"raw_affiliation_string":"Laboratoire IBISC \u2013 FRE CNRS 2873. CNRS, Universit\u00e9 d'Evry Val-d'Essonne, Evry, France","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I88467170"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5091493314","display_name":"Fariza Tahi","orcid":"https://orcid.org/0000-0002-3975-5668"},"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/I88467170","display_name":"Universit\u00e9 d'\u00c9vry Val-d'Essonne","ror":"https://ror.org/00e96v939","country_code":"FR","type":"education","lineage":["https://openalex.org/I277688954","https://openalex.org/I88467170"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Fariza Tahi","raw_affiliation_strings":["Laboratoire IBISC \u2013 FRE CNRS 2873. CNRS, Universit\u00e9 d'Evry Val-d'Essonne, Genopole. 523, place des Terrasses, 91000, Evry, France","Laboratoire IBISC \u2013 FRE CNRS 2873. CNRS, Universit\u00e9 d'Evry Val-d'Essonne, Evry, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratoire IBISC \u2013 FRE CNRS 2873. CNRS, Universit\u00e9 d'Evry Val-d'Essonne, Genopole. 523, place des Terrasses, 91000, Evry, France","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I88467170"]},{"raw_affiliation_string":"Laboratoire IBISC \u2013 FRE CNRS 2873. CNRS, Universit\u00e9 d'Evry Val-d'Essonne, Evry, France","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I88467170"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5091493314"],"corresponding_institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I88467170"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":0.3772,"has_fulltext":true,"cited_by_count":13,"citation_normalized_percentile":{"value":0.59885161,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"8","issue":"1","first_page":"464","last_page":"464"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9894000291824341,"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":0.9894000291824341,"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":0.0015999999595806003,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.00139999995008111,"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/protein-superfamily","display_name":"Protein superfamily","score":0.6514302492141724},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.6155341267585754},{"id":"https://openalex.org/keywords/nucleic-acid-secondary-structure","display_name":"Nucleic acid secondary structure","score":0.6056250333786011},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5779678821563721},{"id":"https://openalex.org/keywords/homologous-chromosome","display_name":"Homologous chromosome","score":0.5686272978782654},{"id":"https://openalex.org/keywords/protein-secondary-structure","display_name":"Protein secondary structure","score":0.567452609539032},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.5460817813873291},{"id":"https://openalex.org/keywords/pseudoknot","display_name":"Pseudoknot","score":0.5093361139297485},{"id":"https://openalex.org/keywords/multiple-sequence-alignment","display_name":"Multiple sequence alignment","score":0.5068319439888},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4960087239742279},{"id":"https://openalex.org/keywords/alignment-free-sequence-analysis","display_name":"Alignment-free sequence analysis","score":0.47939133644104004},{"id":"https://openalex.org/keywords/nucleic-acid-structure","display_name":"Nucleic acid structure","score":0.46841922402381897},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.4568231701850891},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.4479415714740753},{"id":"https://openalex.org/keywords/selection","display_name":"Selection (genetic algorithm)","score":0.4352070689201355},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.4284641146659851},{"id":"https://openalex.org/keywords/structural-alignment","display_name":"Structural alignment","score":0.42386484146118164},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.35052257776260376},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.3410923480987549},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.26361143589019775},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.18973153829574585},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.16095539927482605},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.14266902208328247}],"concepts":[{"id":"https://openalex.org/C178180057","wikidata":"https://www.wikidata.org/wiki/Q7251477","display_name":"Protein superfamily","level":3,"score":0.6514302492141724},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.6155341267585754},{"id":"https://openalex.org/C85468374","wikidata":"https://www.wikidata.org/wiki/Q6589957","display_name":"Nucleic acid secondary structure","level":4,"score":0.6056250333786011},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5779678821563721},{"id":"https://openalex.org/C64894306","wikidata":"https://www.wikidata.org/wiki/Q849622","display_name":"Homologous chromosome","level":3,"score":0.5686272978782654},{"id":"https://openalex.org/C62614982","wikidata":"https://www.wikidata.org/wiki/Q904984","display_name":"Protein secondary structure","level":2,"score":0.567452609539032},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.5460817813873291},{"id":"https://openalex.org/C105130999","wikidata":"https://www.wikidata.org/wiki/Q414976","display_name":"Pseudoknot","level":4,"score":0.5093361139297485},{"id":"https://openalex.org/C88031987","wikidata":"https://www.wikidata.org/wiki/Q1377767","display_name":"Multiple sequence alignment","level":5,"score":0.5068319439888},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4960087239742279},{"id":"https://openalex.org/C180384323","wikidata":"https://www.wikidata.org/wiki/Q16335137","display_name":"Alignment-free sequence analysis","level":5,"score":0.47939133644104004},{"id":"https://openalex.org/C126142528","wikidata":"https://www.wikidata.org/wiki/Q3771876","display_name":"Nucleic acid structure","level":4,"score":0.46841922402381897},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4568231701850891},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.4479415714740753},{"id":"https://openalex.org/C81917197","wikidata":"https://www.wikidata.org/wiki/Q628760","display_name":"Selection (genetic algorithm)","level":2,"score":0.4352070689201355},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.4284641146659851},{"id":"https://openalex.org/C4668613","wikidata":"https://www.wikidata.org/wiki/Q4116110","display_name":"Structural alignment","level":5,"score":0.42386484146118164},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.35052257776260376},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.3410923480987549},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.26361143589019775},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.18973153829574585},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.16095539927482605},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.14266902208328247},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","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":"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":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017385","descriptor_name":"Sequence Homology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017385","descriptor_name":"Sequence Homology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017385","descriptor_name":"Sequence Homology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020029","descriptor_name":"Base Pairing","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020029","descriptor_name":"Base Pairing","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020029","descriptor_name":"Base Pairing","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1186/1471-2105-8-464","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-8-464","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-8-464","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:18045491","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/18045491","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:HAL:hal-00341931v1","is_oa":false,"landing_page_url":"https://hal.science/hal-00341931","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, 2007, 8, pp.Elec. Proc. ⟨10.1186/1471-2105-8-464⟩","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:HAL:hal-00361249v1","is_oa":false,"landing_page_url":"https://hal.science/hal-00361249","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"6th Asia Pacific Bioinformatics Conference (APBC 2008), Jan 2008, Kyoto, Japan. (elec. proc)","raw_type":"info:eu-repo/semantics/conferenceObject"},{"id":"pmh:oai:doaj.org/article:df33c6341e1f44e39eea2d3134145c5b","is_oa":false,"landing_page_url":"https://doaj.org/article/df33c6341e1f44e39eea2d3134145c5b","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 8, Iss 1, p 464 (2007)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:1832851","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2238770","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-8-464","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-8-464","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-8-464","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":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2043192186.pdf","grobid_xml":"https://content.openalex.org/works/W2043192186.grobid-xml"},"referenced_works_count":38,"referenced_works":["https://openalex.org/W149500278","https://openalex.org/W1502958771","https://openalex.org/W1503189902","https://openalex.org/W1585306636","https://openalex.org/W1822377315","https://openalex.org/W1930443964","https://openalex.org/W1950410402","https://openalex.org/W1972402383","https://openalex.org/W1981184189","https://openalex.org/W1984987205","https://openalex.org/W1989481652","https://openalex.org/W2000191287","https://openalex.org/W2001916877","https://openalex.org/W2009818318","https://openalex.org/W2013465290","https://openalex.org/W2017313617","https://openalex.org/W2023209608","https://openalex.org/W2038253050","https://openalex.org/W2043020016","https://openalex.org/W2095145214","https://openalex.org/W2099359200","https://openalex.org/W2100271852","https://openalex.org/W2102225325","https://openalex.org/W2107432340","https://openalex.org/W2107721261","https://openalex.org/W2108852439","https://openalex.org/W2113368761","https://openalex.org/W2114143204","https://openalex.org/W2134453550","https://openalex.org/W2135158529","https://openalex.org/W2135261987","https://openalex.org/W2137283579","https://openalex.org/W2150539879","https://openalex.org/W2163899891","https://openalex.org/W2468850873","https://openalex.org/W4229641056","https://openalex.org/W4245270879","https://openalex.org/W4251866352"],"related_works":["https://openalex.org/W2015399150","https://openalex.org/W1837794086","https://openalex.org/W2061567716","https://openalex.org/W2042681550","https://openalex.org/W2009133913","https://openalex.org/W2055553856","https://openalex.org/W2505756865","https://openalex.org/W2498689255","https://openalex.org/W2258169709","https://openalex.org/W4386496033"],"abstract_inverted_index":{"BACKGROUND:":[0],"The":[1,56],"secondary":[2,26,185,224],"structure":[3,15,27,102,153,186,225],"of":[4,28,49,79,88,118,123,140,178,187,196,207,218],"an":[5,29,133,213],"RNA":[6,30,219],"must":[7,58],"be":[8,19,65,92,106],"known":[9],"before":[10],"the":[11,25,38,77,116,138,143,176,179,184,228],"relationship":[12],"between":[13],"its":[14],"and":[16,42,160],"function":[17],"can":[18,105],"determined.":[20],"One":[21],"way":[22],"to":[23,32,64,108,115,193],"predict":[24],"is":[31,69,82,126,147,212],"identify":[33],"covarying":[34],"residues":[35],"that":[36,199],"maintain":[37],"pairings":[39],"(Watson-Crick,":[40],"Wobble":[41],"non-canonical":[43],"pairings).":[44],"This":[45,104,121,130],"\"comparative":[46],"approach\"":[47],"consists":[48],"identifying":[50],"mutations":[51,63],"from":[52],"homologous":[53,80,89,197,208,220],"sequence":[54,124,158,172],"alignments.":[55,173],"sequences":[57,81,90,141,198,221],"covary":[59],"enough":[60],"for":[61,94,142,182,215,223],"compensatory":[62],"revealed,":[66],"but":[67],"comparison":[68],"difficult":[70],"if":[71],"they":[72],"are":[73],"too":[74],"different.":[75],"Thus":[76],"choice":[78],"critical.":[83],"While":[84],"many":[85],"possible":[86],"combinations":[87,217],"may":[91],"used":[93],"prediction,":[95],"only":[96],"a":[97],"few":[98],"will":[99],"give":[100],"good":[101],"predictions.":[103],"due":[107],"poor":[109],"quality":[110],"alignment":[111],"in":[112],"stems":[113],"or":[114],"variability":[117],"certain":[119],"sequences.":[120,209],"problem":[122],"selection":[125],"currently":[127],"unsolved.":[128],"RESULTS:":[129],"paper":[131],"describes":[132],"algorithm,":[134],"SSCA,":[135],"which":[136],"measures":[137],"suitability":[139],"comparative":[144,229],"approach.":[145,230],"It":[146],"based":[148,167],"on":[149,157,168,171],"evolutionary":[150],"models":[151],"with":[152,227],"constraints,":[154],"particularly":[155],"those":[156],"variations":[159],"stem":[161],"alignment.":[162],"We":[163,174],"propose":[164],"three":[165],"models,":[166],"different":[169],"constraints":[170],"show":[175],"results":[177],"SSCA":[180,190,211],"algorithm":[181,214],"predicting":[183],"several":[188],"RNAs.":[189],"enabled":[191],"us":[192],"choose":[194],"sets":[195,206],"gave":[200],"better":[201],"predictions":[202,226],"than":[203],"arbitrarily":[204],"chosen":[205],"CONCLUSION:":[210],"selecting":[216],"suitable":[222]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2013,"cited_by_count":1}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}