{"id":"https://openalex.org/W2081843224","doi":"https://doi.org/10.1089/106652701446134","title":"The Practical Use of the <i>A</i> * Algorithm for Exact Multiple Sequence Alignment","display_name":"The Practical Use of the <i>A</i> * Algorithm for Exact Multiple Sequence Alignment","publication_year":2000,"publication_date":"2000-10-01","ids":{"openalex":"https://openalex.org/W2081843224","doi":"https://doi.org/10.1089/106652701446134","mag":"2081843224","pmid":"https://pubmed.ncbi.nlm.nih.gov/11153092"},"language":"en","primary_location":{"id":"doi:10.1089/106652701446134","is_oa":false,"landing_page_url":"https://doi.org/10.1089/106652701446134","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/A5085630372","display_name":"Martin Lermen","orcid":null},"institutions":[{"id":"https://openalex.org/I4210109712","display_name":"Max Planck Institute for Informatics","ror":"https://ror.org/01w19ak89","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210109712"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Martin Lermen","raw_affiliation_strings":["Max Planck Institut f\u00fcr Informatik, Im Stadtwald, D-66123 Saarbr\u00fccken, Germany"],"affiliations":[{"raw_affiliation_string":"Max Planck Institut f\u00fcr Informatik, Im Stadtwald, D-66123 Saarbr\u00fccken, Germany","institution_ids":["https://openalex.org/I4210109712"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5078948324","display_name":"Knut Reinert","orcid":"https://orcid.org/0000-0003-3078-8129"},"institutions":[{"id":"https://openalex.org/I4210109712","display_name":"Max Planck Institute for Informatics","ror":"https://ror.org/01w19ak89","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210109712"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Knut Reinert","raw_affiliation_strings":["Max Planck Institut f\u00fcr Informatik, Im Stadtwald, D-66123 Saarbr\u00fccken, Germany"],"affiliations":[{"raw_affiliation_string":"Max Planck Institut f\u00fcr Informatik, Im Stadtwald, D-66123 Saarbr\u00fccken, Germany","institution_ids":["https://openalex.org/I4210109712"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5085630372"],"corresponding_institution_ids":["https://openalex.org/I4210109712"],"apc_list":null,"apc_paid":null,"fwci":3.5887,"has_fulltext":false,"cited_by_count":34,"citation_normalized_percentile":{"value":0.93148102,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"7","issue":"5","first_page":"655","last_page":"671"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.9993000030517578,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.9993000030517578,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","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"}},{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9966999888420105,"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/bounding-overwatch","display_name":"Bounding overwatch","score":0.8102215528488159},{"id":"https://openalex.org/keywords/computation","display_name":"Computation","score":0.7281886339187622},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.7071105241775513},{"id":"https://openalex.org/keywords/shortest-path-problem","display_name":"Shortest path problem","score":0.6725888252258301},{"id":"https://openalex.org/keywords/floyd\u2013warshall-algorithm","display_name":"Floyd\u2013Warshall algorithm","score":0.5644265413284302},{"id":"https://openalex.org/keywords/path","display_name":"Path (computing)","score":0.562702476978302},{"id":"https://openalex.org/keywords/dynamic-programming","display_name":"Dynamic programming","score":0.5439742207527161},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5263784527778625},{"id":"https://openalex.org/keywords/k-shortest-path-routing","display_name":"K shortest path routing","score":0.51363605260849},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.5008420944213867},{"id":"https://openalex.org/keywords/directed-graph","display_name":"Directed graph","score":0.46639010310173035},{"id":"https://openalex.org/keywords/enhanced-data-rates-for-gsm-evolution","display_name":"Enhanced Data Rates for GSM Evolution","score":0.4116692841053009},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.3820054531097412},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.3500159978866577},{"id":"https://openalex.org/keywords/mathematical-optimization","display_name":"Mathematical optimization","score":0.34671926498413086},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.2308962345123291},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.07174926996231079}],"concepts":[{"id":"https://openalex.org/C63584917","wikidata":"https://www.wikidata.org/wiki/Q333286","display_name":"Bounding overwatch","level":2,"score":0.8102215528488159},{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.7281886339187622},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.7071105241775513},{"id":"https://openalex.org/C22590252","wikidata":"https://www.wikidata.org/wiki/Q1058754","display_name":"Shortest path problem","level":3,"score":0.6725888252258301},{"id":"https://openalex.org/C186065694","wikidata":"https://www.wikidata.org/wiki/Q1047576","display_name":"Floyd\u2013Warshall algorithm","level":5,"score":0.5644265413284302},{"id":"https://openalex.org/C2777735758","wikidata":"https://www.wikidata.org/wiki/Q817765","display_name":"Path (computing)","level":2,"score":0.562702476978302},{"id":"https://openalex.org/C37404715","wikidata":"https://www.wikidata.org/wiki/Q380679","display_name":"Dynamic programming","level":2,"score":0.5439742207527161},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5263784527778625},{"id":"https://openalex.org/C70266271","wikidata":"https://www.wikidata.org/wiki/Q6343044","display_name":"K shortest path routing","level":4,"score":0.51363605260849},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5008420944213867},{"id":"https://openalex.org/C146380142","wikidata":"https://www.wikidata.org/wiki/Q1137726","display_name":"Directed graph","level":2,"score":0.46639010310173035},{"id":"https://openalex.org/C162307627","wikidata":"https://www.wikidata.org/wiki/Q204833","display_name":"Enhanced Data Rates for GSM Evolution","level":2,"score":0.4116692841053009},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.3820054531097412},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.3500159978866577},{"id":"https://openalex.org/C126255220","wikidata":"https://www.wikidata.org/wiki/Q141495","display_name":"Mathematical optimization","level":1,"score":0.34671926498413086},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.2308962345123291},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.07174926996231079},{"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/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","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}],"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":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid 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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"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":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D017386","descriptor_name":"Sequence Homology, Amino Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017386","descriptor_name":"Sequence Homology, Amino Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017386","descriptor_name":"Sequence Homology, Amino Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1089/106652701446134","is_oa":false,"landing_page_url":"https://doi.org/10.1089/106652701446134","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:11153092","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/11153092","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":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":13,"referenced_works":["https://openalex.org/W1494580035","https://openalex.org/W1589993665","https://openalex.org/W1783219955","https://openalex.org/W1974326986","https://openalex.org/W1990061958","https://openalex.org/W1998139877","https://openalex.org/W2002638840","https://openalex.org/W2041397659","https://openalex.org/W2047923658","https://openalex.org/W2074231493","https://openalex.org/W2156153879","https://openalex.org/W2158598102","https://openalex.org/W2913618495"],"related_works":["https://openalex.org/W2354846196","https://openalex.org/W4293054712","https://openalex.org/W2391130892","https://openalex.org/W2360981904","https://openalex.org/W2348761196","https://openalex.org/W4313182153","https://openalex.org/W2347245430","https://openalex.org/W1617152041","https://openalex.org/W2392078542","https://openalex.org/W1519427079"],"abstract_inverted_index":{"Multiple":[0],"alignment":[1],"is":[2,10,47,136],"an":[3],"important":[4],"problem":[5],"in":[6,25,35,77,96],"computational":[7],"biology.":[8],"It":[9],"well":[11],"known":[12],"that":[13,50,110,126],"it":[14,144],"can":[15,27,118],"be":[16,28],"solved":[17],"exactly":[18],"by":[19,59],"a":[20,31,36,48,56,78,132],"dynamic":[21],"programming":[22],"algorithm":[23,42,76,129],"which":[24],"turn":[26],"interpreted":[29],"as":[30],"shortest":[32,57,70],"path":[33,58],"computation":[34,54],"directed":[37],"acyclic":[38],"graph.":[39],"The":[40],"A*":[41,75,112,128],"(or":[43],"goal-directed":[44],"unidirectional":[45],"search)":[46],"technique":[49,135],"speeds":[51],"up":[52,120],"the":[53,61,66,69,74,111,127,139],"of":[55,68],"transforming":[60],"edge":[62],"lengths":[63],"without":[64],"losing":[65],"optimality":[67],"path.":[71],"We":[72,94],"implemented":[73],"computer":[79],"program":[80,98],"similar":[81],"to":[82,138],"MSA":[83],"(Gupta":[84],"et":[85],"al.,":[86],"1995)":[87],"and":[88,91,105,108],"FMA":[89],"(Shibuya":[90],"Imai,":[92],"1997).":[93],"incorporated":[95],"this":[97],"new":[99],"bounding":[100,134,142],"strategies":[101],"for":[102],"both":[103],"lower":[104],"upper":[106],"bounds":[107],"show":[109,125],"algorithm,":[113],"together":[114,130],"with":[115,131],"our":[116],"improvements,":[117],"speed":[119],"computations":[121],"considerably.":[122],"Additionally,":[123],"we":[124],"standard":[133],"superior":[137],"well-known":[140],"Carrillo-Lipman":[141],"since":[143],"excludes":[145],"more":[146],"nodes":[147],"from":[148],"consideration.":[149]},"counts_by_year":[{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":2}],"updated_date":"2025-12-23T23:11:35.936235","created_date":"2016-06-24T00:00:00"}
