{"id":"https://openalex.org/W2610493105","doi":"https://doi.org/10.1089/cmb.1998.5.493","title":"Dynamic Programming Alignment Accuracy","display_name":"Dynamic Programming Alignment Accuracy","publication_year":1998,"publication_date":"1998-01-01","ids":{"openalex":"https://openalex.org/W2610493105","doi":"https://doi.org/10.1089/cmb.1998.5.493","mag":"2610493105","pmid":"https://pubmed.ncbi.nlm.nih.gov/9773345"},"language":"en","primary_location":{"id":"doi:10.1089/cmb.1998.5.493","is_oa":false,"landing_page_url":"https://doi.org/10.1089/cmb.1998.5.493","pdf_url":null,"source":{"id":"https://openalex.org/S78571599","display_name":"Journal of Computational Biology","issn_l":"1066-5277","issn":["1066-5277","1557-8666"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320443","host_organization_name":"Mary Ann Liebert, Inc.","host_organization_lineage":["https://openalex.org/P4310320443"],"host_organization_lineage_names":["Mary Ann Liebert, Inc."],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","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/A5054625887","display_name":"Ian Holmes","orcid":"https://orcid.org/0000-0001-7639-5369"},"institutions":[{"id":"https://openalex.org/I2802476451","display_name":"Wellcome Sanger Institute","ror":"https://ror.org/05cy4wa09","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I2802476451","https://openalex.org/I87048295"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"IAN HOLMES","raw_affiliation_strings":["Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge, England. ihh,rd@sanger.ac.uk"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge, England. ihh,rd@sanger.ac.uk","institution_ids":["https://openalex.org/I2802476451"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5082040351","display_name":"Richard Durbin","orcid":"https://orcid.org/0000-0002-9130-1006"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"RICHARD DURBIN","raw_affiliation_strings":[""],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.4795,"has_fulltext":false,"cited_by_count":109,"citation_normalized_percentile":{"value":0.6409344,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"5","issue":"3","first_page":"493","last_page":"504"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","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/T10015","display_name":"Genomics and Phylogenetic Studies","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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9973999857902527,"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/T10602","display_name":"Glycosylation and Glycoproteins Research","score":0.9819999933242798,"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/dynamic-programming","display_name":"Dynamic programming","score":0.7812615633010864},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6558870077133179},{"id":"https://openalex.org/keywords/path","display_name":"Path (computing)","score":0.6057969927787781},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.6011365652084351},{"id":"https://openalex.org/keywords/measure","display_name":"Measure (data warehouse)","score":0.5785484313964844},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.5300148725509644},{"id":"https://openalex.org/keywords/multiple-sequence-alignment","display_name":"Multiple sequence alignment","score":0.520982563495636},{"id":"https://openalex.org/keywords/series","display_name":"Series (stratigraphy)","score":0.5071346759796143},{"id":"https://openalex.org/keywords/enhanced-data-rates-for-gsm-evolution","display_name":"Enhanced Data Rates for GSM Evolution","score":0.4218355715274811},{"id":"https://openalex.org/keywords/standard-deviation","display_name":"Standard deviation","score":0.4121789038181305},{"id":"https://openalex.org/keywords/mathematical-optimization","display_name":"Mathematical optimization","score":0.3278385400772095},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.29987847805023193},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2596389949321747},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.2509664297103882},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.1951744258403778},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.11944261193275452}],"concepts":[{"id":"https://openalex.org/C37404715","wikidata":"https://www.wikidata.org/wiki/Q380679","display_name":"Dynamic programming","level":2,"score":0.7812615633010864},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6558870077133179},{"id":"https://openalex.org/C2777735758","wikidata":"https://www.wikidata.org/wiki/Q817765","display_name":"Path (computing)","level":2,"score":0.6057969927787781},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.6011365652084351},{"id":"https://openalex.org/C2780009758","wikidata":"https://www.wikidata.org/wiki/Q6804172","display_name":"Measure (data warehouse)","level":2,"score":0.5785484313964844},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5300148725509644},{"id":"https://openalex.org/C88031987","wikidata":"https://www.wikidata.org/wiki/Q1377767","display_name":"Multiple sequence alignment","level":5,"score":0.520982563495636},{"id":"https://openalex.org/C143724316","wikidata":"https://www.wikidata.org/wiki/Q312468","display_name":"Series (stratigraphy)","level":2,"score":0.5071346759796143},{"id":"https://openalex.org/C162307627","wikidata":"https://www.wikidata.org/wiki/Q204833","display_name":"Enhanced Data Rates for GSM Evolution","level":2,"score":0.4218355715274811},{"id":"https://openalex.org/C22679943","wikidata":"https://www.wikidata.org/wiki/Q159375","display_name":"Standard deviation","level":2,"score":0.4121789038181305},{"id":"https://openalex.org/C126255220","wikidata":"https://www.wikidata.org/wiki/Q141495","display_name":"Mathematical optimization","level":1,"score":0.3278385400772095},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.29987847805023193},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2596389949321747},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.2509664297103882},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.1951744258403778},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.11944261193275452},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"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/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"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/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","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":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011336","descriptor_name":"Probability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011336","descriptor_name":"Probability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011336","descriptor_name":"Probability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","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":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1089/cmb.1998.5.493","is_oa":false,"landing_page_url":"https://doi.org/10.1089/cmb.1998.5.493","pdf_url":null,"source":{"id":"https://openalex.org/S78571599","display_name":"Journal of Computational Biology","issn_l":"1066-5277","issn":["1066-5277","1557-8666"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320443","host_organization_name":"Mary Ann Liebert, Inc.","host_organization_lineage":["https://openalex.org/P4310320443"],"host_organization_lineage_names":["Mary Ann Liebert, Inc."],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computational Biology","raw_type":"journal-article"},{"id":"pmid:9773345","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/9773345","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":"Journal of computational biology : a journal of computational molecular cell biology","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320311904","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08"},{"id":"https://openalex.org/F4320334626","display_name":"Medical Research Council","ror":"https://ror.org/03x94j517"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":10,"referenced_works":["https://openalex.org/W1500214331","https://openalex.org/W2015292449","https://openalex.org/W2021839440","https://openalex.org/W2055043387","https://openalex.org/W2071749306","https://openalex.org/W2074231493","https://openalex.org/W2087064593","https://openalex.org/W2089966120","https://openalex.org/W2101418959","https://openalex.org/W2134595458"],"related_works":["https://openalex.org/W1591831971","https://openalex.org/W2367862442","https://openalex.org/W2348501199","https://openalex.org/W88386512","https://openalex.org/W3000366369","https://openalex.org/W1646393397","https://openalex.org/W1608334680","https://openalex.org/W2369537633","https://openalex.org/W1578673849","https://openalex.org/W2350198651"],"abstract_inverted_index":{"Algorithms":[0],"for":[1,79],"generating":[2],"alignments":[3,19,124],"of":[4,17,28,52,64,101],"biological":[5],"sequences":[6],"have":[7],"inherent":[8],"statistical":[9],"limitations":[10],"when":[11],"it":[12,38],"comes":[13],"to":[14,49,96,112],"the":[15,18,26,29,50,53,58,62,98],"accuracy":[16,27,74,100,116],"they":[20],"produce.":[21],"Using":[22],"simulations,":[23],"we":[24,93],"measure":[25],"standard":[30,126],"global":[31],"dynamic":[32,127],"programming":[33,128],"method":[34],"and":[35,84,89,105],"show":[36,106],"that":[37],"can":[39,76,109],"be":[40,77,110],"reasonably":[41],"well":[42],"modelled":[43],"by":[44],"an":[45,114],"\"edge":[46],"wander\"":[47],"approximation":[48],"distribution":[51],"optimal":[54,115],"scoring":[55,82],"path":[56,60],"around":[57],"correct":[59],"in":[61,130],"vicinity":[63],"a":[65,70,102],"gap.":[66],"We":[67],"also":[68],"give":[69],"table":[71],"from":[72],"which":[73,119],"values":[75],"predicted":[78],"commonly":[80],"used":[81,111],"schemes":[83],"sequence":[85],"divergences":[86],"(the":[87],"PAM":[88],"BLOSUM":[90],"series).":[91],"Finally":[92],"describe":[94],"how":[95,107],"calculate":[97],"expected":[99],"given":[103],"alignment,":[104],"this":[108],"construct":[113],"alignment":[117],"algorithm":[118],"generates":[120],"significantly":[121],"more":[122],"accurate":[123],"than":[125],"methods":[129],"simulated":[131],"experiments.":[132]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":9},{"year":2021,"cited_by_count":7},{"year":2020,"cited_by_count":5},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":6},{"year":2013,"cited_by_count":4},{"year":2012,"cited_by_count":2}],"updated_date":"2026-01-13T01:12:25.745995","created_date":"2025-10-10T00:00:00"}