{"id":"https://openalex.org/W1990853496","doi":"https://doi.org/10.1371/journal.pcbi.0030056","title":"Query-Dependent Banding (QDB) for Faster RNA Similarity Searches","display_name":"Query-Dependent Banding (QDB) for Faster RNA Similarity Searches","publication_year":2007,"publication_date":"2007-03-28","ids":{"openalex":"https://openalex.org/W1990853496","doi":"https://doi.org/10.1371/journal.pcbi.0030056","mag":"1990853496","pmid":"https://pubmed.ncbi.nlm.nih.gov/17397253"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.0030056","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.0030056","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.0030056&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.0030056&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5021155495","display_name":"Eric P. Nawrocki","orcid":"https://orcid.org/0000-0002-2497-3427"},"institutions":[{"id":"https://openalex.org/I195573530","display_name":"Janelia Research Campus","ror":"https://ror.org/013sk6x84","country_code":"US","type":"facility","lineage":["https://openalex.org/I1344073410","https://openalex.org/I195573530"]},{"id":"https://openalex.org/I1344073410","display_name":"Howard Hughes Medical Institute","ror":"https://ror.org/006w34k90","country_code":"US","type":"facility","lineage":["https://openalex.org/I1344073410"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Eric P Nawrocki","raw_affiliation_strings":["Howard Hughes Medical Institute, Janelia Farm Research Campus, Ashburn, Virginia, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Howard Hughes Medical Institute, Janelia Farm Research Campus, Ashburn, Virginia, United States of America","institution_ids":["https://openalex.org/I195573530","https://openalex.org/I1344073410"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5020118397","display_name":"Sean R. Eddy","orcid":"https://orcid.org/0000-0001-6676-4706"},"institutions":[{"id":"https://openalex.org/I195573530","display_name":"Janelia Research Campus","ror":"https://ror.org/013sk6x84","country_code":"US","type":"facility","lineage":["https://openalex.org/I1344073410","https://openalex.org/I195573530"]},{"id":"https://openalex.org/I1344073410","display_name":"Howard Hughes Medical Institute","ror":"https://ror.org/006w34k90","country_code":"US","type":"facility","lineage":["https://openalex.org/I1344073410"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Sean R Eddy","raw_affiliation_strings":["Howard Hughes Medical Institute, Janelia Farm Research Campus, Ashburn, Virginia, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Howard Hughes Medical Institute, Janelia Farm Research Campus, Ashburn, Virginia, United States of America","institution_ids":["https://openalex.org/I195573530","https://openalex.org/I1344073410"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5020118397"],"corresponding_institution_ids":["https://openalex.org/I1344073410","https://openalex.org/I195573530"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":8.2983,"has_fulltext":true,"cited_by_count":298,"citation_normalized_percentile":{"value":0.98519627,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":95,"max":100},"biblio":{"volume":"3","issue":"3","first_page":"e56","last_page":"e56"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9998999834060669,"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":0.9998999834060669,"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":0.9998000264167786,"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/T11482","display_name":"RNA modifications and cancer","score":0.9975000023841858,"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/probabilistic-logic","display_name":"Probabilistic logic","score":0.6733225584030151},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6543058156967163},{"id":"https://openalex.org/keywords/speedup","display_name":"Speedup","score":0.6226415038108826},{"id":"https://openalex.org/keywords/dynamic-programming","display_name":"Dynamic programming","score":0.5407426953315735},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.46776315569877625},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3942565321922302},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3764890134334564},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.36584776639938354},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.3233110308647156},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.17911231517791748},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.13337409496307373}],"concepts":[{"id":"https://openalex.org/C49937458","wikidata":"https://www.wikidata.org/wiki/Q2599292","display_name":"Probabilistic logic","level":2,"score":0.6733225584030151},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6543058156967163},{"id":"https://openalex.org/C68339613","wikidata":"https://www.wikidata.org/wiki/Q1549489","display_name":"Speedup","level":2,"score":0.6226415038108826},{"id":"https://openalex.org/C37404715","wikidata":"https://www.wikidata.org/wiki/Q380679","display_name":"Dynamic programming","level":2,"score":0.5407426953315735},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.46776315569877625},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3942565321922302},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3764890134334564},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.36584776639938354},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.3233110308647156},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.17911231517791748},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.13337409496307373},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"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":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"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":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012689","descriptor_name":"Sequence Homology, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012689","descriptor_name":"Sequence Homology, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012689","descriptor_name":"Sequence Homology, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012689","descriptor_name":"Sequence Homology, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","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":"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":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","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":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":6,"locations":[{"id":"doi:10.1371/journal.pcbi.0030056","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.0030056","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.0030056&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},{"id":"pmid:17397253","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/17397253","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.279.4534","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.279.4534","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/8f/3c/PLoS_Comput_Biol_2007_Mar_30_3(3)_e56.tar.gz","raw_type":"text"},{"id":"pmh:oai:RePEc:plo:pcbi00:0030056","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.0030056","pdf_url":null,"source":{"id":"https://openalex.org/S4306401271","display_name":"RePEc: Research Papers in Economics","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I77793887","host_organization_name":"Federal Reserve Bank of St. Louis","host_organization_lineage":["https://openalex.org/I77793887"],"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":"article"},{"id":"pmh:oai:doaj.org/article:46b87bf7b95742eea9b85404cba9d591","is_oa":true,"landing_page_url":"https://doaj.org/article/46b87bf7b95742eea9b85404cba9d591","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":"PLoS Computational Biology, Vol 3, Iss 3, p e56 (2007)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:1847999","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/1847999","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.0030056","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.0030056","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.0030056&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3411168983","display_name":null,"funder_award_id":"R01-HG01363","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"},{"id":"https://openalex.org/G3975758957","display_name":null,"funder_award_id":"T32-HG000045","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"},{"id":"https://openalex.org/G4506430185","display_name":null,"funder_award_id":"HG000045","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4741369470","display_name":null,"funder_award_id":"R01 HG001363","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"},{"id":"https://openalex.org/G5812753170","display_name":null,"funder_award_id":"HG000045","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"},{"id":"https://openalex.org/G8859818835","display_name":null,"funder_award_id":"T32 HG000045","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"}],"funders":[{"id":"https://openalex.org/F4320309650","display_name":"Washington University in St. Louis","ror":"https://ror.org/01yc7t268"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337348","display_name":"National Human Genome Research Institute","ror":"https://ror.org/00baak391"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1990853496.pdf","grobid_xml":"https://content.openalex.org/works/W1990853496.grobid-xml"},"referenced_works_count":45,"referenced_works":["https://openalex.org/W421997344","https://openalex.org/W1502621331","https://openalex.org/W1523895109","https://openalex.org/W1574109141","https://openalex.org/W1872483787","https://openalex.org/W1950410402","https://openalex.org/W1965998064","https://openalex.org/W1967517087","https://openalex.org/W1970961429","https://openalex.org/W1973578915","https://openalex.org/W1976765586","https://openalex.org/W1996053875","https://openalex.org/W2002089154","https://openalex.org/W2009570821","https://openalex.org/W2011368877","https://openalex.org/W2023206235","https://openalex.org/W2025305823","https://openalex.org/W2042881722","https://openalex.org/W2058044724","https://openalex.org/W2064345118","https://openalex.org/W2076992251","https://openalex.org/W2086204534","https://openalex.org/W2102066220","https://openalex.org/W2105070391","https://openalex.org/W2109119231","https://openalex.org/W2115457188","https://openalex.org/W2116520841","https://openalex.org/W2120242947","https://openalex.org/W2120523244","https://openalex.org/W2122665495","https://openalex.org/W2124871329","https://openalex.org/W2131538597","https://openalex.org/W2134597758","https://openalex.org/W2136280642","https://openalex.org/W2138452362","https://openalex.org/W2139695444","https://openalex.org/W2140244239","https://openalex.org/W2140446903","https://openalex.org/W2149429041","https://openalex.org/W2154649313","https://openalex.org/W2155237411","https://openalex.org/W2158714788","https://openalex.org/W2165230358","https://openalex.org/W2432517183","https://openalex.org/W2981264952"],"related_works":["https://openalex.org/W2058965144","https://openalex.org/W2164382479","https://openalex.org/W2146343568","https://openalex.org/W98480971","https://openalex.org/W2150291671","https://openalex.org/W2013643406","https://openalex.org/W2027972911","https://openalex.org/W2157978810","https://openalex.org/W2597809628","https://openalex.org/W3046370962"],"abstract_inverted_index":{"When":[0],"searching":[1],"sequence":[2,13],"databases":[3],"for":[4,26,104,123],"RNAs,":[5],"it":[6],"is":[7],"desirable":[8],"to":[9,62,102,131],"score":[10],"both":[11],"primary":[12],"and":[14,111,146],"RNA":[15,27,107,125],"secondary":[16],"structure":[17],"similarity.":[18],"Covariance":[19],"models":[20,24],"(CMs)":[21],"are":[22],"probabilistic":[23,59],"well-suited":[25],"similarity":[28],"search":[29],"applications.":[30],"However,":[31],"the":[32,58,66,76,84,92],"computational":[33],"complexity":[34,96],"of":[35,65,75,97,108,115],"CM":[36,61,98],"dynamic":[37,67],"programming":[38,68],"alignment":[39,99],"algorithms":[40],"has":[41],"limited":[42],"their":[43],"practical":[44],"application.":[45],"Here":[46],"we":[47],"describe":[48],"an":[49],"acceleration":[50],"method":[51],"called":[52],"query-dependent":[53],"banding":[54],"(QDB),":[55],"which":[56],"uses":[57],"query":[60,106],"precalculate":[63],"regions":[64],"lattice":[69],"that":[70],"have":[71,80],"negligible":[72],"probability,":[73],"independently":[74],"target":[77,113],"database.":[78],"We":[79],"implemented":[81],"QDB":[82,90],"in":[83,119],"freely":[85],"available":[86],"Infernal":[87],"software":[88],"package.":[89],"reduces":[91],"average":[93],"case":[94],"time":[95],"from":[100,149],"LN(2.4)":[101],"LN(1.3)":[103],"a":[105,112,120],"N":[109],"residues":[110],"database":[114],"L":[116],"residues,":[117],"resulting":[118,148],"4-fold":[121],"speedup":[122],"typical":[124],"queries.":[126],"Combined":[127],"with":[128],"other":[129],"improvements":[130],"Infernal,":[132],"including":[133],"informative":[134],"mixture":[135],"Dirichlet":[136],"priors":[137],"on":[138],"model":[139],"parameters,":[140],"benchmarks":[141],"also":[142],"show":[143],"increased":[144],"sensitivity":[145],"specificity":[147],"improved":[150],"parameterization.":[151]},"counts_by_year":[{"year":2024,"cited_by_count":8},{"year":2023,"cited_by_count":8},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":7},{"year":2019,"cited_by_count":16},{"year":2018,"cited_by_count":20},{"year":2017,"cited_by_count":27},{"year":2016,"cited_by_count":19},{"year":2015,"cited_by_count":29},{"year":2014,"cited_by_count":18},{"year":2013,"cited_by_count":24},{"year":2012,"cited_by_count":29}],"updated_date":"2026-07-15T18:14:33.161393","created_date":"2025-10-10T00:00:00"}
