{"id":"https://openalex.org/W2139449083","doi":"https://doi.org/10.1093/bioinformatics/btp580","title":"CentroidAlign: fast and accurate aligner for structured RNAs by maximizing expected sum-of-pairs score","display_name":"CentroidAlign: fast and accurate aligner for structured RNAs by maximizing expected sum-of-pairs score","publication_year":2009,"publication_date":"2009-10-06","ids":{"openalex":"https://openalex.org/W2139449083","doi":"https://doi.org/10.1093/bioinformatics/btp580","mag":"2139449083","pmid":"https://pubmed.ncbi.nlm.nih.gov/19808876"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btp580","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp580","pdf_url":null,"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":null,"license_id":null,"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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5025857432","display_name":"Michiaki Hamada","orcid":"https://orcid.org/0000-0001-9466-1034"},"institutions":[{"id":"https://openalex.org/I4210104082","display_name":"Japan Biological Informatics Consortium","ror":"https://ror.org/01astg473","country_code":"JP","type":"nonprofit","lineage":["https://openalex.org/I4210104082"]},{"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"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Michiaki Hamada","raw_affiliation_strings":["1 Mizuho Information & Research Institute, Inc, 2\u20133 Kanda-Nishikicho, Chiyoda-ku, Tokyo 101\u20138443, 2Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2\u201341\u20136, Aomi, Koto-ku, Tokyo 135\u20130064, 3Japan Biological Informatics Consortium, 2\u201345 Aomi, Koto-ku, Tokyo 135\u20138073 and 4Graduate School of Frontier Sciences, University of Tokyo, 5\u20131\u20135 Kashiwanoha, Kashiwa 277\u20138562, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Mizuho Information & Research Institute, Inc, 2\u20133 Kanda-Nishikicho, Chiyoda-ku, Tokyo 101\u20138443, 2Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2\u201341\u20136, Aomi, Koto-ku, Tokyo 135\u20130064, 3Japan Biological Informatics Consortium, 2\u201345 Aomi, Koto-ku, Tokyo 135\u20138073 and 4Graduate School of Frontier Sciences, University of Tokyo, 5\u20131\u20135 Kashiwanoha, Kashiwa 277\u20138562, Japan","institution_ids":["https://openalex.org/I4210104082","https://openalex.org/I74801974","https://openalex.org/I73613424"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076175043","display_name":"Kengo Sato","orcid":"https://orcid.org/0000-0001-6744-7390"},"institutions":[{"id":"https://openalex.org/I4210104082","display_name":"Japan Biological Informatics Consortium","ror":"https://ror.org/01astg473","country_code":"JP","type":"nonprofit","lineage":["https://openalex.org/I4210104082"]},{"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"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Kengo Sato","raw_affiliation_strings":["1 Mizuho Information & Research Institute, Inc, 2\u20133 Kanda-Nishikicho, Chiyoda-ku, Tokyo 101\u20138443, 2Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2\u201341\u20136, Aomi, Koto-ku, Tokyo 135\u20130064, 3Japan Biological Informatics Consortium, 2\u201345 Aomi, Koto-ku, Tokyo 135\u20138073 and 4Graduate School of Frontier Sciences, University of Tokyo, 5\u20131\u20135 Kashiwanoha, Kashiwa 277\u20138562, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Mizuho Information & Research Institute, Inc, 2\u20133 Kanda-Nishikicho, Chiyoda-ku, Tokyo 101\u20138443, 2Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2\u201341\u20136, Aomi, Koto-ku, Tokyo 135\u20130064, 3Japan Biological Informatics Consortium, 2\u201345 Aomi, Koto-ku, Tokyo 135\u20138073 and 4Graduate School of Frontier Sciences, University of Tokyo, 5\u20131\u20135 Kashiwanoha, Kashiwa 277\u20138562, Japan","institution_ids":["https://openalex.org/I4210104082","https://openalex.org/I74801974","https://openalex.org/I73613424"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024402799","display_name":"Hisanori Kiryu","orcid":"https://orcid.org/0000-0003-3554-5353"},"institutions":[{"id":"https://openalex.org/I4210104082","display_name":"Japan Biological Informatics Consortium","ror":"https://ror.org/01astg473","country_code":"JP","type":"nonprofit","lineage":["https://openalex.org/I4210104082"]},{"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"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Hisanori Kiryu","raw_affiliation_strings":["1 Mizuho Information & Research Institute, Inc, 2\u20133 Kanda-Nishikicho, Chiyoda-ku, Tokyo 101\u20138443, 2Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2\u201341\u20136, Aomi, Koto-ku, Tokyo 135\u20130064, 3Japan Biological Informatics Consortium, 2\u201345 Aomi, Koto-ku, Tokyo 135\u20138073 and 4Graduate School of Frontier Sciences, University of Tokyo, 5\u20131\u20135 Kashiwanoha, Kashiwa 277\u20138562, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Mizuho Information & Research Institute, Inc, 2\u20133 Kanda-Nishikicho, Chiyoda-ku, Tokyo 101\u20138443, 2Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2\u201341\u20136, Aomi, Koto-ku, Tokyo 135\u20130064, 3Japan Biological Informatics Consortium, 2\u201345 Aomi, Koto-ku, Tokyo 135\u20138073 and 4Graduate School of Frontier Sciences, University of Tokyo, 5\u20131\u20135 Kashiwanoha, Kashiwa 277\u20138562, Japan","institution_ids":["https://openalex.org/I4210104082","https://openalex.org/I74801974","https://openalex.org/I73613424"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015688097","display_name":"Toutai Mituyama","orcid":"https://orcid.org/0000-0002-1110-6375"},"institutions":[{"id":"https://openalex.org/I4210104082","display_name":"Japan Biological Informatics Consortium","ror":"https://ror.org/01astg473","country_code":"JP","type":"nonprofit","lineage":["https://openalex.org/I4210104082"]},{"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"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Toutai Mituyama","raw_affiliation_strings":["1 Mizuho Information & Research Institute, Inc, 2\u20133 Kanda-Nishikicho, Chiyoda-ku, Tokyo 101\u20138443, 2Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2\u201341\u20136, Aomi, Koto-ku, Tokyo 135\u20130064, 3Japan Biological Informatics Consortium, 2\u201345 Aomi, Koto-ku, Tokyo 135\u20138073 and 4Graduate School of Frontier Sciences, University of Tokyo, 5\u20131\u20135 Kashiwanoha, Kashiwa 277\u20138562, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Mizuho Information & Research Institute, Inc, 2\u20133 Kanda-Nishikicho, Chiyoda-ku, Tokyo 101\u20138443, 2Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2\u201341\u20136, Aomi, Koto-ku, Tokyo 135\u20130064, 3Japan Biological Informatics Consortium, 2\u201345 Aomi, Koto-ku, Tokyo 135\u20138073 and 4Graduate School of Frontier Sciences, University of Tokyo, 5\u20131\u20135 Kashiwanoha, Kashiwa 277\u20138562, Japan","institution_ids":["https://openalex.org/I4210104082","https://openalex.org/I74801974","https://openalex.org/I73613424"]}]},{"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/I4210104082","display_name":"Japan Biological Informatics Consortium","ror":"https://ror.org/01astg473","country_code":"JP","type":"nonprofit","lineage":["https://openalex.org/I4210104082"]},{"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"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Kiyoshi Asai","raw_affiliation_strings":["1 Mizuho Information & Research Institute, Inc, 2\u20133 Kanda-Nishikicho, Chiyoda-ku, Tokyo 101\u20138443, 2Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2\u201341\u20136, Aomi, Koto-ku, Tokyo 135\u20130064, 3Japan Biological Informatics Consortium, 2\u201345 Aomi, Koto-ku, Tokyo 135\u20138073 and 4Graduate School of Frontier Sciences, University of Tokyo, 5\u20131\u20135 Kashiwanoha, Kashiwa 277\u20138562, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Mizuho Information & Research Institute, Inc, 2\u20133 Kanda-Nishikicho, Chiyoda-ku, Tokyo 101\u20138443, 2Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2\u201341\u20136, Aomi, Koto-ku, Tokyo 135\u20130064, 3Japan Biological Informatics Consortium, 2\u201345 Aomi, Koto-ku, Tokyo 135\u20138073 and 4Graduate School of Frontier Sciences, University of Tokyo, 5\u20131\u20135 Kashiwanoha, Kashiwa 277\u20138562, Japan","institution_ids":["https://openalex.org/I4210104082","https://openalex.org/I74801974","https://openalex.org/I73613424"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5025857432"],"corresponding_institution_ids":["https://openalex.org/I4210104082","https://openalex.org/I73613424","https://openalex.org/I74801974"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":2.3268,"has_fulltext":false,"cited_by_count":51,"citation_normalized_percentile":{"value":0.88479631,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"25","issue":"24","first_page":"3236","last_page":"3243"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9553999900817871,"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":0.9553999900817871,"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":0.014499999582767487,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.006399999838322401,"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/pairwise-comparison","display_name":"Pairwise comparison","score":0.8093191385269165},{"id":"https://openalex.org/keywords/estimator","display_name":"Estimator","score":0.757885754108429},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.6560273170471191},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6421574950218201},{"id":"https://openalex.org/keywords/consistency","display_name":"Consistency (knowledge bases)","score":0.5782379508018494},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5244660377502441},{"id":"https://openalex.org/keywords/probabilistic-logic","display_name":"Probabilistic logic","score":0.4908960461616516},{"id":"https://openalex.org/keywords/transformation","display_name":"Transformation (genetics)","score":0.4381810426712036},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.41811931133270264},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.33779293298721313},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.32517221570014954},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.23317819833755493},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.20520243048667908},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.17607495188713074},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.16961583495140076}],"concepts":[{"id":"https://openalex.org/C184898388","wikidata":"https://www.wikidata.org/wiki/Q1435712","display_name":"Pairwise comparison","level":2,"score":0.8093191385269165},{"id":"https://openalex.org/C185429906","wikidata":"https://www.wikidata.org/wiki/Q1130160","display_name":"Estimator","level":2,"score":0.757885754108429},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.6560273170471191},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6421574950218201},{"id":"https://openalex.org/C2776436953","wikidata":"https://www.wikidata.org/wiki/Q5163215","display_name":"Consistency (knowledge bases)","level":2,"score":0.5782379508018494},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5244660377502441},{"id":"https://openalex.org/C49937458","wikidata":"https://www.wikidata.org/wiki/Q2599292","display_name":"Probabilistic logic","level":2,"score":0.4908960461616516},{"id":"https://openalex.org/C204241405","wikidata":"https://www.wikidata.org/wiki/Q461499","display_name":"Transformation (genetics)","level":3,"score":0.4381810426712036},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.41811931133270264},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.33779293298721313},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.32517221570014954},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.23317819833755493},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.20520243048667908},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.17607495188713074},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.16961583495140076},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0}],"mesh":[{"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":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","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":"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},{"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":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D022661","descriptor_name":"RNA, Untranslated","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D022661","descriptor_name":"RNA, Untranslated","qualifier_ui":"Q000378","qualifier_name":"metabolism","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},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btp580","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp580","pdf_url":null,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:19808876","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19808876","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:t2r2.star.titech.ac.jp:50744911","is_oa":false,"landing_page_url":"http://t2r2.star.titech.ac.jp/cgi-bin/publicationinfo.cgi?q_publication_content_number=CTT100937989","pdf_url":null,"source":{"id":"https://openalex.org/S4377196385","display_name":"Tokyo Tech Research Repository (Tokyo Institute of Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I114531698","host_organization_name":"Tokyo Institute of Technology","host_organization_lineage":["https://openalex.org/I114531698"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Journal Article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":51,"referenced_works":["https://openalex.org/W1489075871","https://openalex.org/W1522740115","https://openalex.org/W1861164398","https://openalex.org/W1866859902","https://openalex.org/W1909512798","https://openalex.org/W1981584745","https://openalex.org/W1984675364","https://openalex.org/W1988512789","https://openalex.org/W1993324010","https://openalex.org/W1994958179","https://openalex.org/W1997631042","https://openalex.org/W2001876475","https://openalex.org/W2003062976","https://openalex.org/W2011289056","https://openalex.org/W2018216725","https://openalex.org/W2038079502","https://openalex.org/W2049283139","https://openalex.org/W2069792162","https://openalex.org/W2071749306","https://openalex.org/W2074231493","https://openalex.org/W2087064593","https://openalex.org/W2095145214","https://openalex.org/W2099383450","https://openalex.org/W2101497682","https://openalex.org/W2101535367","https://openalex.org/W2102017611","https://openalex.org/W2103899452","https://openalex.org/W2110845345","https://openalex.org/W2111272410","https://openalex.org/W2115215562","https://openalex.org/W2118829610","https://openalex.org/W2121691652","https://openalex.org/W2122035121","https://openalex.org/W2127688908","https://openalex.org/W2128109027","https://openalex.org/W2131054067","https://openalex.org/W2140302584","https://openalex.org/W2140872496","https://openalex.org/W2141411594","https://openalex.org/W2141411672","https://openalex.org/W2141670298","https://openalex.org/W2142038007","https://openalex.org/W2142116796","https://openalex.org/W2142768277","https://openalex.org/W2151994495","https://openalex.org/W2163798335","https://openalex.org/W2166486463","https://openalex.org/W2170945060","https://openalex.org/W2610493105","https://openalex.org/W3214380909","https://openalex.org/W4245668478"],"related_works":["https://openalex.org/W2487162673","https://openalex.org/W2378211422","https://openalex.org/W2949152769","https://openalex.org/W2029032313","https://openalex.org/W4315563560","https://openalex.org/W2553559590","https://openalex.org/W2117163556","https://openalex.org/W2171766007","https://openalex.org/W2143990275","https://openalex.org/W108653788"],"abstract_inverted_index":{"MOTIVATION:":[0],"The":[1,133,208],"importance":[2],"of":[3,8,32,51,60,74,84,92,120,131,139,197,204,216],"accurate":[4],"and":[5,123,126,142,156,193],"fast":[6],"predictions":[7,33],"multiple":[9,49,202],"alignments":[10,50,93,143,160,173,203],"for":[11,37,48,71,201],"RNA":[12,75],"sequences":[13,122],"has":[14],"increased":[15],"due":[16],"to":[17],"recent":[18],"findings":[19],"about":[20],"functional":[21],"non-coding":[22],"RNAs.":[23,206],"Recent":[24],"studies":[25],"suggest":[26],"that":[27,144,185],"maximizing":[28,56],"the":[29,57,65,79,97,103,118,153,158,167,175,186,195,217],"expected":[30,58,67,80],"accuracy":[31,59,68],"will":[34],"be":[35],"useful":[36],"many":[38,198],"problems":[39],"in":[40,147,219],"bioinformatics.":[41],"RESULTS:":[42],"We":[43],"designed":[44],"a":[45,85,89,190],"novel":[46],"estimator":[47,70,109,135],"structured":[52,205],"RNAs,":[53],"based":[54],"on":[55,172,225],"predictions.":[61],"First,":[62],"we":[63,106,165],"define":[64],"maximum":[66],"(MEA)":[69],"pairwise":[72,159],"alignment":[73,87],"sequences.":[76,163],"This":[77],"maximizes":[78],"sum-of-pairs":[81],"score":[82],"(SPS)":[83],"predicted":[86],"under":[88],"probability":[90],"distribution":[91],"given":[94],"by":[95,101],"marginalizing":[96],"Sankoff":[98],"model.":[99],"Then,":[100],"approximating":[102],"MEA":[104],"estimator,":[105],"obtain":[107],"an":[108,214],"whose":[110],"time":[111],"complexity":[112],"is":[113,117,213,222],"O(L(3)+c(2)dL(2))":[114],"where":[115],"L":[116],"length":[119],"input":[121,162],"both":[124],"c":[125],"d":[127],"are":[128,145,235],"constants":[129],"independent":[130],"L.":[132],"proposed":[134,176,187],"can":[136],"handle":[137],"uncertainty":[138],"secondary":[140,154],"structures":[141,155],"obstacles":[146],"Bioinformatics":[148,238],"because":[149],"it":[150],"considers":[151],"all":[152,157],"as":[161],"Moreover,":[164],"integrate":[166],"probabilistic":[168],"consistency":[169],"transformation":[170],"(PCT)":[171],"into":[174],"estimator.":[177],"Computational":[178],"experiments":[179],"using":[180],"six":[181],"benchmark":[182],"datasets":[183],"indicate":[184],"method":[188],"achieved":[189],"favorable":[191],"SPS":[192],"was":[194],"fastest":[196],"state-of-the-art":[199],"tools":[200],"AVAILABILITY:":[207],"software":[209],"called":[210],"CentroidAlign,":[211],"which":[212],"implementation":[215],"algorithm":[218],"this":[220],"article,":[221],"freely":[223],"available":[224,236],"our":[226],"website:":[227],"http://www.ncrna.org/software/centroidalign/.":[228],"CONTACT:":[229],"hamada-michiaki@aist.go.jp":[230],"SUPPLEMENTARY":[231],"INFORMATION:":[232],"Supplementary":[233],"data":[234],"at":[237],"online.":[239]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":4},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":6},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":5},{"year":2012,"cited_by_count":7}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}