{"id":"https://openalex.org/W2029848394","doi":"https://doi.org/10.1109/tevc.2011.2162849","title":"Progressive Alignment Method Using Genetic Algorithm for Multiple Sequence Alignment","display_name":"Progressive Alignment Method Using Genetic Algorithm for Multiple Sequence Alignment","publication_year":2012,"publication_date":"2012-02-10","ids":{"openalex":"https://openalex.org/W2029848394","doi":"https://doi.org/10.1109/tevc.2011.2162849","mag":"2029848394"},"language":"en","primary_location":{"id":"doi:10.1109/tevc.2011.2162849","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tevc.2011.2162849","pdf_url":null,"source":{"id":"https://openalex.org/S93787993","display_name":"IEEE Transactions on Evolutionary Computation","issn_l":"1089-778X","issn":["1089-778X","1941-0026"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Evolutionary Computation","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"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/A5109141727","display_name":"Farhana Naznin","orcid":null},"institutions":[{"id":"https://openalex.org/I40053085","display_name":"Australian Defence Force Academy","ror":"https://ror.org/02j5s7g39","country_code":"AU","type":"education","lineage":["https://openalex.org/I31746571","https://openalex.org/I40053085","https://openalex.org/I4394709116"]},{"id":"https://openalex.org/I31746571","display_name":"UNSW Sydney","ror":"https://ror.org/03r8z3t63","country_code":"AU","type":"education","lineage":["https://openalex.org/I31746571"]},{"id":"https://openalex.org/I4394709116","display_name":"UNSW Canberra","ror":"https://ror.org/0125wpx05","country_code":null,"type":"education","lineage":["https://openalex.org/I31746571","https://openalex.org/I4394709116"]}],"countries":["AU"],"is_corresponding":true,"raw_author_name":"Farhana Naznin","raw_affiliation_strings":["School of Engineering and Information Technology at Australian Defense Force Academy, University of New South Wales, Canberra, Australia","[School of Engineering and Information Technology, University of New South, Wales Canberra, ACT, Australia]"],"affiliations":[{"raw_affiliation_string":"School of Engineering and Information Technology at Australian Defense Force Academy, University of New South Wales, Canberra, Australia","institution_ids":["https://openalex.org/I40053085"]},{"raw_affiliation_string":"[School of Engineering and Information Technology, University of New South, Wales Canberra, ACT, Australia]","institution_ids":["https://openalex.org/I31746571","https://openalex.org/I4394709116"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027440671","display_name":"Ruhul Sarker","orcid":"https://orcid.org/0000-0002-1363-2774"},"institutions":[{"id":"https://openalex.org/I40053085","display_name":"Australian Defence Force Academy","ror":"https://ror.org/02j5s7g39","country_code":"AU","type":"education","lineage":["https://openalex.org/I31746571","https://openalex.org/I40053085","https://openalex.org/I4394709116"]},{"id":"https://openalex.org/I4394709116","display_name":"UNSW Canberra","ror":"https://ror.org/0125wpx05","country_code":null,"type":"education","lineage":["https://openalex.org/I31746571","https://openalex.org/I4394709116"]},{"id":"https://openalex.org/I31746571","display_name":"UNSW Sydney","ror":"https://ror.org/03r8z3t63","country_code":"AU","type":"education","lineage":["https://openalex.org/I31746571"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Ruhul Sarker","raw_affiliation_strings":["School of Engineering and Information Technology at Australian Defense Force Academy, University of New South Wales, Canberra, Australia","[School of Engineering and Information Technology, University of New South, Wales Canberra, ACT, Australia]"],"affiliations":[{"raw_affiliation_string":"School of Engineering and Information Technology at Australian Defense Force Academy, University of New South Wales, Canberra, Australia","institution_ids":["https://openalex.org/I40053085"]},{"raw_affiliation_string":"[School of Engineering and Information Technology, University of New South, Wales Canberra, ACT, Australia]","institution_ids":["https://openalex.org/I31746571","https://openalex.org/I4394709116"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5003507463","display_name":"Daryl Essam","orcid":"https://orcid.org/0000-0002-6923-7079"},"institutions":[{"id":"https://openalex.org/I40053085","display_name":"Australian Defence Force Academy","ror":"https://ror.org/02j5s7g39","country_code":"AU","type":"education","lineage":["https://openalex.org/I31746571","https://openalex.org/I40053085","https://openalex.org/I4394709116"]},{"id":"https://openalex.org/I31746571","display_name":"UNSW Sydney","ror":"https://ror.org/03r8z3t63","country_code":"AU","type":"education","lineage":["https://openalex.org/I31746571"]},{"id":"https://openalex.org/I4394709116","display_name":"UNSW Canberra","ror":"https://ror.org/0125wpx05","country_code":null,"type":"education","lineage":["https://openalex.org/I31746571","https://openalex.org/I4394709116"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Daryl Essam","raw_affiliation_strings":["School of Engineering and Information Technology at Australian Defense Force Academy, University of New South Wales, Canberra, Australia","[School of Engineering and Information Technology, University of New South, Wales Canberra, ACT, Australia]"],"affiliations":[{"raw_affiliation_string":"School of Engineering and Information Technology at Australian Defense Force Academy, University of New South Wales, Canberra, Australia","institution_ids":["https://openalex.org/I40053085"]},{"raw_affiliation_string":"[School of Engineering and Information Technology, University of New South, Wales Canberra, ACT, Australia]","institution_ids":["https://openalex.org/I31746571","https://openalex.org/I4394709116"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5109141727"],"corresponding_institution_ids":["https://openalex.org/I31746571","https://openalex.org/I40053085","https://openalex.org/I4394709116"],"apc_list":null,"apc_paid":null,"fwci":1.9701,"has_fulltext":false,"cited_by_count":67,"citation_normalized_percentile":{"value":0.85876163,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"16","issue":"5","first_page":"615","last_page":"631"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.998199999332428,"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":0.998199999332428,"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/T11269","display_name":"Algorithms and Data Compression","score":0.9865000247955322,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9761999845504761,"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/shuffling","display_name":"Shuffling","score":0.7356420159339905},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.6960110068321228},{"id":"https://openalex.org/keywords/multiple-sequence-alignment","display_name":"Multiple sequence alignment","score":0.6918371915817261},{"id":"https://openalex.org/keywords/genetic-algorithm","display_name":"Genetic algorithm","score":0.6719428896903992},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6214913129806519},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.564508318901062},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.5532292723655701},{"id":"https://openalex.org/keywords/alignment-free-sequence-analysis","display_name":"Alignment-free sequence analysis","score":0.4878575801849365},{"id":"https://openalex.org/keywords/population","display_name":"Population","score":0.4513489603996277},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.4219086170196533},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.1880628764629364},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.07679948210716248}],"concepts":[{"id":"https://openalex.org/C167927819","wikidata":"https://www.wikidata.org/wiki/Q1930567","display_name":"Shuffling","level":2,"score":0.7356420159339905},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.6960110068321228},{"id":"https://openalex.org/C88031987","wikidata":"https://www.wikidata.org/wiki/Q1377767","display_name":"Multiple sequence alignment","level":5,"score":0.6918371915817261},{"id":"https://openalex.org/C8880873","wikidata":"https://www.wikidata.org/wiki/Q187787","display_name":"Genetic algorithm","level":2,"score":0.6719428896903992},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6214913129806519},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.564508318901062},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5532292723655701},{"id":"https://openalex.org/C180384323","wikidata":"https://www.wikidata.org/wiki/Q16335137","display_name":"Alignment-free sequence analysis","level":5,"score":0.4878575801849365},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.4513489603996277},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.4219086170196533},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.1880628764629364},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.07679948210716248},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","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/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0},{"id":"https://openalex.org/C149923435","wikidata":"https://www.wikidata.org/wiki/Q37732","display_name":"Demography","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/C144024400","wikidata":"https://www.wikidata.org/wiki/Q21201","display_name":"Sociology","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/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/tevc.2011.2162849","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tevc.2011.2162849","pdf_url":null,"source":{"id":"https://openalex.org/S93787993","display_name":"IEEE Transactions on Evolutionary Computation","issn_l":"1089-778X","issn":["1089-778X","1941-0026"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Evolutionary Computation","raw_type":"journal-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":60,"referenced_works":["https://openalex.org/W11515763","https://openalex.org/W155968654","https://openalex.org/W1484713061","https://openalex.org/W1527979595","https://openalex.org/W1693576464","https://openalex.org/W1702013544","https://openalex.org/W1905425803","https://openalex.org/W1964918240","https://openalex.org/W1969153299","https://openalex.org/W1980913156","https://openalex.org/W1982693868","https://openalex.org/W1990554768","https://openalex.org/W1998300401","https://openalex.org/W2006273041","https://openalex.org/W2008518635","https://openalex.org/W2009310436","https://openalex.org/W2022788172","https://openalex.org/W2044164898","https://openalex.org/W2050802973","https://openalex.org/W2052831012","https://openalex.org/W2064856647","https://openalex.org/W2065461553","https://openalex.org/W2066504777","https://openalex.org/W2068083406","https://openalex.org/W2074231493","https://openalex.org/W2085251576","https://openalex.org/W2087064593","https://openalex.org/W2097382368","https://openalex.org/W2097706568","https://openalex.org/W2101418959","https://openalex.org/W2102502076","https://openalex.org/W2102785645","https://openalex.org/W2102941368","https://openalex.org/W2106882534","https://openalex.org/W2110291136","https://openalex.org/W2122369731","https://openalex.org/W2128070230","https://openalex.org/W2128356721","https://openalex.org/W2128442209","https://openalex.org/W2128613007","https://openalex.org/W2129437793","https://openalex.org/W2132926880","https://openalex.org/W2140872496","https://openalex.org/W2141411672","https://openalex.org/W2143210482","https://openalex.org/W2144362290","https://openalex.org/W2146338925","https://openalex.org/W2148311769","https://openalex.org/W2149208773","https://openalex.org/W2152331922","https://openalex.org/W2155237411","https://openalex.org/W2163860567","https://openalex.org/W2171963266","https://openalex.org/W3150945973","https://openalex.org/W4241025692","https://openalex.org/W6600477597","https://openalex.org/W6606305083","https://openalex.org/W6637200175","https://openalex.org/W6639918947","https://openalex.org/W6678068712"],"related_works":["https://openalex.org/W2051969447","https://openalex.org/W2133116680","https://openalex.org/W2111937814","https://openalex.org/W2141411672","https://openalex.org/W2091678889","https://openalex.org/W1482324242","https://openalex.org/W187239587","https://openalex.org/W88386512","https://openalex.org/W2730968108","https://openalex.org/W4386770652"],"abstract_inverted_index":{"In":[0],"this":[1],"paper,":[2],"we":[3,69,128],"have":[4,21,57,70,129],"proposed":[5,168],"a":[6,11,105,115],"progressive":[7],"alignment":[8],"method":[9,169],"using":[10],"genetic":[12,55,94],"algorithm":[13],"for":[14,154],"multiple":[15],"sequence":[16],"alignment,":[17],"named":[18],"GAPAM.":[19,61],"We":[20],"introduced":[22],"two":[23,140],"new":[24],"mechanisms":[25],"to":[26,35],"generate":[27,36],"an":[28],"initial":[29],"population:":[30],"the":[31,44,48,64,119,135,152,157,163,167,171],"first":[32],"mechanism":[33],"is":[34,46],"guide":[37],"trees":[38],"with":[39,60,73,118],"randomly":[40],"selected":[41],"sequences":[42,49],"and":[43,86,88,101,126,159],"second":[45],"shuffling":[47],"inside":[50],"such":[51,77,97,123],"trees.":[52],"Two":[53],"different":[54],"operators":[56],"been":[58],"implemented":[59],"To":[62,113],"test":[63],"performance":[65,165],"of":[66,107,156,166],"our":[67],"algorithm,":[68],"compared":[71],"it":[72],"existing":[74],"well-known":[75],"methods,":[76,91],"as":[78,98,124],"PRRP,":[79],"CLUSTALX,":[80],"DIALIGN,":[81],"HMMT,":[82],"SB_PIMA,":[83],"ML_PIMA,":[84],"MULTALIGN,":[85],"PILEUP8,":[87],"also":[89,160],"other":[90,172],"based":[92,121],"on":[93],"algorithms":[95,122],"(GA),":[96],"SAGA,":[99],"MSA-GA,":[100],"RBT-GA,":[102,127],"by":[103,138],"solving":[104],"number":[106],"benchmark":[108],"datasets":[109,136],"from":[110],"BAliBase":[111],"2.0.":[112],"make":[114],"fairer":[116],"comparison":[117],"GA":[120],"MSA-GA":[125],"performed":[130],"further":[131],"experiments":[132],"covering":[133],"all":[134],"reported":[137],"those":[139],"algorithms.":[141],"The":[142],"experimental":[143],"results":[144],"showed":[145],"that":[146,162],"GAPAM":[147],"achieved":[148],"better":[149],"solutions":[150],"than":[151],"others":[153],"most":[155],"cases,":[158],"revealed":[161],"overall":[164],"outperformed":[170],"methods":[173],"mentioned":[174],"above.":[175]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":5},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":5},{"year":2018,"cited_by_count":6},{"year":2017,"cited_by_count":6},{"year":2016,"cited_by_count":14},{"year":2015,"cited_by_count":5},{"year":2014,"cited_by_count":7},{"year":2013,"cited_by_count":3}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
