{"id":"https://openalex.org/W2103899452","doi":"https://doi.org/10.1093/bioinformatics/btm146","title":"Murlet: a practical multiple alignment tool for structural RNA sequences","display_name":"Murlet: a practical multiple alignment tool for structural RNA sequences","publication_year":2007,"publication_date":"2007-04-25","ids":{"openalex":"https://openalex.org/W2103899452","doi":"https://doi.org/10.1093/bioinformatics/btm146","mag":"2103899452","pmid":"https://pubmed.ncbi.nlm.nih.gov/17459961"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btm146","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btm146","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/23/13/1588/23703848/btm146.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/23/13/1588/23703848/btm146.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5024402799","display_name":"Hisanori Kiryu","orcid":"https://orcid.org/0000-0003-3554-5353"},"institutions":[{"id":"https://openalex.org/I73613424","display_name":"National Institute of Advanced Industrial Science and Technology","ror":"https://ror.org/01703db54","country_code":"JP","type":"government","lineage":["https://openalex.org/I73613424"]},{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]},{"id":"https://openalex.org/I75917431","display_name":"Nara Institute of Science and Technology","ror":"https://ror.org/05bhada84","country_code":"JP","type":"education","lineage":["https://openalex.org/I75917431"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Hisanori Kiryu","raw_affiliation_strings":["1 Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2-42 Aomi, Koto-ku, Tokyo 135-0064, 2Graduate School of Information Sciences, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192 and 3Department of Computational Biology, Faculty of Frontier Science, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8561, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2-42 Aomi, Koto-ku, Tokyo 135-0064, 2Graduate School of Information Sciences, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192 and 3Department of Computational Biology, Faculty of Frontier Science, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8561, Japan","institution_ids":["https://openalex.org/I73613424","https://openalex.org/I74801974","https://openalex.org/I75917431"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021642801","display_name":"Yasuo Tabei","orcid":"https://orcid.org/0000-0003-2368-5607"},"institutions":[{"id":"https://openalex.org/I73613424","display_name":"National Institute of Advanced Industrial Science and Technology","ror":"https://ror.org/01703db54","country_code":"JP","type":"government","lineage":["https://openalex.org/I73613424"]},{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]},{"id":"https://openalex.org/I75917431","display_name":"Nara Institute of Science and Technology","ror":"https://ror.org/05bhada84","country_code":"JP","type":"education","lineage":["https://openalex.org/I75917431"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Yasuo Tabei","raw_affiliation_strings":["1 Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2-42 Aomi, Koto-ku, Tokyo 135-0064, 2Graduate School of Information Sciences, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192 and 3Department of Computational Biology, Faculty of Frontier Science, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8561, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2-42 Aomi, Koto-ku, Tokyo 135-0064, 2Graduate School of Information Sciences, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192 and 3Department of Computational Biology, Faculty of Frontier Science, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8561, Japan","institution_ids":["https://openalex.org/I73613424","https://openalex.org/I74801974","https://openalex.org/I75917431"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5109004340","display_name":"Taishin Kin","orcid":null},"institutions":[{"id":"https://openalex.org/I73613424","display_name":"National Institute of Advanced Industrial Science and Technology","ror":"https://ror.org/01703db54","country_code":"JP","type":"government","lineage":["https://openalex.org/I73613424"]},{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]},{"id":"https://openalex.org/I75917431","display_name":"Nara Institute of Science and Technology","ror":"https://ror.org/05bhada84","country_code":"JP","type":"education","lineage":["https://openalex.org/I75917431"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Taishin Kin","raw_affiliation_strings":["1 Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2-42 Aomi, Koto-ku, Tokyo 135-0064, 2Graduate School of Information Sciences, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192 and 3Department of Computational Biology, Faculty of Frontier Science, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8561, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2-42 Aomi, Koto-ku, Tokyo 135-0064, 2Graduate School of Information Sciences, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192 and 3Department of Computational Biology, Faculty of Frontier Science, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8561, Japan","institution_ids":["https://openalex.org/I73613424","https://openalex.org/I74801974","https://openalex.org/I75917431"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5082068847","display_name":"Kiyoshi Asai","orcid":"https://orcid.org/0000-0003-0909-4982"},"institutions":[{"id":"https://openalex.org/I73613424","display_name":"National Institute of Advanced Industrial Science and Technology","ror":"https://ror.org/01703db54","country_code":"JP","type":"government","lineage":["https://openalex.org/I73613424"]},{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]},{"id":"https://openalex.org/I75917431","display_name":"Nara Institute of Science and Technology","ror":"https://ror.org/05bhada84","country_code":"JP","type":"education","lineage":["https://openalex.org/I75917431"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Kiyoshi Asai","raw_affiliation_strings":["1 Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2-42 Aomi, Koto-ku, Tokyo 135-0064, 2Graduate School of Information Sciences, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192 and 3Department of Computational Biology, Faculty of Frontier Science, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8561, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2-42 Aomi, Koto-ku, Tokyo 135-0064, 2Graduate School of Information Sciences, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192 and 3Department of Computational Biology, Faculty of Frontier Science, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8561, Japan","institution_ids":["https://openalex.org/I73613424","https://openalex.org/I74801974","https://openalex.org/I75917431"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5024402799"],"corresponding_institution_ids":["https://openalex.org/I73613424","https://openalex.org/I74801974","https://openalex.org/I75917431"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":3.8972,"has_fulltext":true,"cited_by_count":76,"citation_normalized_percentile":{"value":0.94508925,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"23","issue":"13","first_page":"1588","last_page":"1598"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9617000222206116,"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":0.9617000222206116,"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":0.01769999973475933,"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":0.003599999938160181,"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/multiple-sequence-alignment","display_name":"Multiple sequence alignment","score":0.7399914264678955},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6945224404335022},{"id":"https://openalex.org/keywords/structural-alignment","display_name":"Structural alignment","score":0.635680615901947},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.6128460764884949},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.5878705382347107},{"id":"https://openalex.org/keywords/alignment-free-sequence-analysis","display_name":"Alignment-free sequence analysis","score":0.575562596321106},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.5146404504776001},{"id":"https://openalex.org/keywords/nucleic-acid-secondary-structure","display_name":"Nucleic acid secondary structure","score":0.51031893491745},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.48229506611824036},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.4452379047870636},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.23004543781280518},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1910591423511505},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1510385274887085},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.08343997597694397}],"concepts":[{"id":"https://openalex.org/C88031987","wikidata":"https://www.wikidata.org/wiki/Q1377767","display_name":"Multiple sequence alignment","level":5,"score":0.7399914264678955},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6945224404335022},{"id":"https://openalex.org/C4668613","wikidata":"https://www.wikidata.org/wiki/Q4116110","display_name":"Structural alignment","level":5,"score":0.635680615901947},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.6128460764884949},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.5878705382347107},{"id":"https://openalex.org/C180384323","wikidata":"https://www.wikidata.org/wiki/Q16335137","display_name":"Alignment-free sequence analysis","level":5,"score":0.575562596321106},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.5146404504776001},{"id":"https://openalex.org/C85468374","wikidata":"https://www.wikidata.org/wiki/Q6589957","display_name":"Nucleic acid secondary structure","level":4,"score":0.51031893491745},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.48229506611824036},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.4452379047870636},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.23004543781280518},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1910591423511505},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1510385274887085},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.08343997597694397},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","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":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btm146","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btm146","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/23/13/1588/23703848/btm146.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:17459961","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/17459961","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:10.1.1.799.9325","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.799.9325","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.jsbi.org/pdfs/journal1/GIW06/GIW06P073.pdf","raw_type":"text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btm146","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btm146","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/23/13/1588/23703848/btm146.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2103899452.pdf","grobid_xml":"https://content.openalex.org/works/W2103899452.grobid-xml"},"referenced_works_count":38,"referenced_works":["https://openalex.org/W1522740115","https://openalex.org/W1622263187","https://openalex.org/W1822105579","https://openalex.org/W1909512798","https://openalex.org/W1974326986","https://openalex.org/W1984675364","https://openalex.org/W1986234964","https://openalex.org/W2009570821","https://openalex.org/W2009736453","https://openalex.org/W2009818318","https://openalex.org/W2018216725","https://openalex.org/W2054849588","https://openalex.org/W2071749306","https://openalex.org/W2085115334","https://openalex.org/W2095145214","https://openalex.org/W2099468911","https://openalex.org/W2102017611","https://openalex.org/W2103225674","https://openalex.org/W2103250001","https://openalex.org/W2106882534","https://openalex.org/W2109553965","https://openalex.org/W2122035121","https://openalex.org/W2128356721","https://openalex.org/W2130032853","https://openalex.org/W2137076005","https://openalex.org/W2137640371","https://openalex.org/W2140651796","https://openalex.org/W2140872496","https://openalex.org/W2149820283","https://openalex.org/W2154845231","https://openalex.org/W2158381555","https://openalex.org/W2158826174","https://openalex.org/W2166745309","https://openalex.org/W2610493105","https://openalex.org/W3214380909","https://openalex.org/W4232524617","https://openalex.org/W4242931615","https://openalex.org/W4245668478"],"related_works":["https://openalex.org/W2051969447","https://openalex.org/W2029514038","https://openalex.org/W2111937814","https://openalex.org/W2141411672","https://openalex.org/W1482324242","https://openalex.org/W1985408726","https://openalex.org/W2468116983","https://openalex.org/W2088487249","https://openalex.org/W187239587","https://openalex.org/W2055553856"],"abstract_inverted_index":{"MOTIVATION:":[0],"Structural":[1],"RNA":[2,29,65,79,211,220],"genes":[3],"exhibit":[4],"unique":[5],"evolutionary":[6],"patterns":[7,17],"that":[8,39,97,119,176,204,221],"are":[9,142,193,268,276],"designed":[10],"to":[11,63,145],"conserve":[12],"their":[13],"secondary":[14,162,187],"structures;":[15],"these":[16],"should":[18],"be":[19],"taken":[20],"into":[21],"account":[22],"while":[23],"constructing":[24],"accurate":[25],"multiple":[26,75,228],"alignments":[27],"of":[28,43,56,77,86,123,164,184,230,256],"genes.":[30],"The":[31,242,252],"Sankoff":[32,58,88,151],"algorithm":[33,38,59,72,82,113,156,206,243],"is":[34,83,222,244],"a":[35,84],"natural":[36],"alignment":[37,48,76,109,148,166,179,192,229],"includes":[40],"the":[41,47,51,57,74,87,99,108,115,121,132,147,150,160,165,172,178,182,185,194,197,215,247,257,261],"effect":[42],"base-pair":[44],"covariation":[45],"in":[46,226,246,265],"model.":[49],"However,":[50],"extremely":[52],"high":[53],"computational":[54],"cost":[55],"precludes":[60],"its":[61],"application":[62],"most":[64],"sequences.":[66,80],"RESULTS:":[67],"We":[68,174,201],"propose":[69],"an":[70,93],"efficient":[71,94],"for":[73,137,171],"structural":[78],"Our":[81],"variant":[85],"algorithm,":[89],"and":[90,101,181,260],"it":[91],"uses":[92,168],"scoring":[95],"system":[96],"reduces":[98],"time":[100],"space":[102],"requirements":[103],"considerably":[104],"without":[105],"compromising":[106],"on":[107],"quality.":[110],"First,":[111],"our":[112,155,191,205],"computes":[114],"match":[116],"probability":[117,135],"matrix":[118,136],"measures":[120],"alignability":[122],"each":[124,138],"position":[125],"pair":[126],"between":[127],"sequences":[128,212,232],"as":[129,131,214],"well":[130],"base":[133],"pairing":[134],"sequence.":[139],"These":[140],"probabilities":[141],"then":[143],"combined":[144],"score":[146],"using":[149,238],"algorithm.":[152],"By":[153],"itself,":[154],"does":[157],"not":[158,234],"predict":[159],"consensus":[161,186],"structure":[163,188],"but":[167],"external":[169],"programs":[170,199],"prediction.":[173],"demonstrate":[175,203],"both":[177],"quality":[180],"accuracy":[183],"prediction":[189],"from":[190],"highest":[195],"among":[196],"other":[198,239],"examined.":[200],"also":[202],"can":[207],"align":[208],"relatively":[209],"long":[210],"such":[213,231],"eukaryotic-type":[216],"signal":[217],"recognition":[218],"particle":[219],"approximately":[223],"300":[224],"nt":[225],"length;":[227],"has":[233],"been":[235],"possible":[236],"by":[237],"Sankoff-based":[240],"algorithms.":[241],"implemented":[245],"software":[248,259],"named":[249],"'Murlet'.":[250],"AVAILABILITY:":[251],"C++":[253],"source":[254],"code":[255],"Murlet":[258],"test":[262],"dataset":[263],"used":[264],"this":[266],"study":[267],"available":[269,277],"at":[270,278],"http://www.ncrna.org/papers/Murlet/.":[271],"SUPPLEMENTARY":[272],"INFORMATION:":[273],"Supplementary":[274],"data":[275],"Bioinformatics":[279],"online.":[280]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":3},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":4},{"year":2014,"cited_by_count":4},{"year":2013,"cited_by_count":5},{"year":2012,"cited_by_count":7}],"updated_date":"2026-07-22T07:51:19.307946","created_date":"2025-10-10T00:00:00"}
