{"id":"https://openalex.org/W2144935903","doi":"https://doi.org/10.1093/bib/bbk008","title":"Pairwise sequence alignment\u2014it's all about us!","display_name":"Pairwise sequence alignment\u2014it's all about us!","publication_year":2006,"publication_date":"2006-02-04","ids":{"openalex":"https://openalex.org/W2144935903","doi":"https://doi.org/10.1093/bib/bbk008","mag":"2144935903","pmid":"https://pubmed.ncbi.nlm.nih.gov/16761368"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbk008","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbk008","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"review","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/A5071466820","display_name":"Lisa Mullan","orcid":null},"institutions":[{"id":"https://openalex.org/I1312486979","display_name":"Local Initiatives Support Corporation","ror":"https://ror.org/04r5g1376","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1312486979"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Lisa Mullan","raw_affiliation_strings":["Lisa Mullan is a Scientific Training Officer at the European Bioinformatics Institute, which she joined in 2004 to coordinate their user training program. Previously she worked as training coordinator at the late Rosalind Franklin Centre for Genome Research (formerly HGMP-RC). She currently also teaches introductory level bioinformatics on courses throughout the world"],"affiliations":[{"raw_affiliation_string":"Lisa Mullan is a Scientific Training Officer at the European Bioinformatics Institute, which she joined in 2004 to coordinate their user training program. Previously she worked as training coordinator at the late Rosalind Franklin Centre for Genome Research (formerly HGMP-RC). She currently also teaches introductory level bioinformatics on courses throughout the world","institution_ids":["https://openalex.org/I1312486979"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5071466820"],"corresponding_institution_ids":["https://openalex.org/I1312486979"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":0.1325,"has_fulltext":false,"cited_by_count":15,"citation_normalized_percentile":{"value":0.52312003,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"7","issue":"1","first_page":"113","last_page":"115"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9997000098228455,"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":0.9997000098228455,"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/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.9810000061988831,"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":0.9650999903678894,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/pairwise-comparison","display_name":"Pairwise comparison","score":0.8610975742340088},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.6429729461669922},{"id":"https://openalex.org/keywords/multiple-sequence-alignment","display_name":"Multiple sequence alignment","score":0.5900910496711731},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5333862900733948},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.3917274475097656},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3741489052772522},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.16216039657592773},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.14496222138404846},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.1382429301738739},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.0628693699836731}],"concepts":[{"id":"https://openalex.org/C184898388","wikidata":"https://www.wikidata.org/wiki/Q1435712","display_name":"Pairwise comparison","level":2,"score":0.8610975742340088},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.6429729461669922},{"id":"https://openalex.org/C88031987","wikidata":"https://www.wikidata.org/wiki/Q1377767","display_name":"Multiple sequence alignment","level":5,"score":0.5900910496711731},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5333862900733948},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.3917274475097656},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3741489052772522},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.16216039657592773},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.14496222138404846},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.1382429301738739},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0628693699836731}],"mesh":[{"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":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":true},{"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":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":true},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":true},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbk008","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbk008","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:16761368","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16761368","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":"Briefings in bioinformatics","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":10,"referenced_works":["https://openalex.org/W2008841836","https://openalex.org/W2031716828","https://openalex.org/W2074231493","https://openalex.org/W2087064593","https://openalex.org/W2108215151","https://openalex.org/W2117249420","https://openalex.org/W2124145810","https://openalex.org/W2135326109","https://openalex.org/W2143210482","https://openalex.org/W6675949863"],"related_works":["https://openalex.org/W2129361631","https://openalex.org/W1591831971","https://openalex.org/W2095439426","https://openalex.org/W2021852343","https://openalex.org/W2295731408","https://openalex.org/W2351540725","https://openalex.org/W2051319991","https://openalex.org/W15200223","https://openalex.org/W2396068618","https://openalex.org/W2045540004"],"abstract_inverted_index":{"Pairwise":[0,22],"alignment":[1,23,101,122,201,450,550],"is":[2,36,63,102,116,190,406,441],"one":[3,149,200,535],"of":[4,9,15,20,73,96,133,144,216,241,322,344,348,359,361,379,384,387,410,426,438,456,466,472,538],"the":[5,56,71,99,109,131,145,157,209,250,269,284,291,307,309,311,314,318,320,330,335,339,341,349,371,377,382,392,400,422,427,432,464,470,473,476,478,482,485,487,493,499,508,526,534,541,548],"most":[6,26,245,435],"fundamental":[7],"tools":[8],"bioinformatics":[10],"and":[11,66,123,159,182,202,257,272,317,337,374,532,556],"underpins":[12],"a":[13,30,87,140,153,160,167,213,238,357,408,444,514],"variety":[14],"other,":[16],"more":[17,350],"sophisticated":[18],"methods":[19],"annotation.":[21],"in":[24,268,290,313,329,370,399,463],"its":[25,120,503],"rigorous":[27],"form":[28],"uses":[29],"method":[31],"called":[32],"\u2018dynamic":[33],"programming\u2019,":[34],"which":[35,85,325,413],"highly":[37],"accurate,":[38],"but":[39],"also":[40,407],"incredibly":[41],"costly":[42],"to":[43,47,59,282,333,390,430,481,511,524,528],"compute.":[44],"In":[45,130,469],"order":[46],"align":[48],"anything":[49],"other":[50,210],"than":[51],"an":[52],"exact":[53],"alphabetic":[54],"match,":[55],"algorithm":[57],"has":[58,496],"know":[60],"what":[61,74],"it":[62,68,75,552],"looking":[64],"for":[65,89,108,152,166,447,516],"how":[67,97],"can":[69,196,396,501],"evaluate":[70],"worth":[72],"finds.":[76],"To":[77],"this":[78,128,439,467],"end,":[79],"\u2018comparison":[80],"matrices\u2019":[81],"have":[82,294,326],"been":[83,295,327,497],"created":[84,267,296,369],"define":[86],"score":[88,111,115,151,165,529,543],"every":[90],"possible":[91],"match":[92,155],"possibility\u2014an":[93],"effective":[94],"tally":[95],"well":[98],"computational":[100],"doing.":[103],"The":[104,113,244,262,305,365,434],"software":[105],"will":[106],"search":[107],"highest":[110,542],"available.":[112],"final":[114],"relevant":[117],"only":[118,220],"with":[119,416],"resulting":[121],"cannot":[124],"be":[125,197,397,512],"used":[126,332,429,462],"outside":[127],"context.":[129],"case":[132,471],"DNA,":[134],"comparison":[135,171,260,494,531],"values":[136,178],"are":[137,184,221,233,249,414],"generated":[138],"using":[139],"simple":[141],"identity":[142,425,460],"matrix":[143,172,265,437,495,505],"type":[146],"that":[147,195,302,454],"allows":[148],"(positive)":[150],"correct":[154],"within":[156,279,381],"alignment,":[158],"different":[161],"(zero":[162],"or":[163,520],"negative)":[164],"mismatch.":[168],"A":[169],"fuller":[170],"allowing":[173],"ambiguities,":[174],"alters":[175],"these":[176],"basic":[177],"as":[179,218,225,231,551],"potential":[180,518],"transitions":[181],"transversions":[183],"taken":[185],"into":[186],"account\u2014but":[187],"essentially":[188],"there":[189,222,232],"very":[191],"little":[192],"mathematical":[193],"difference":[194],"achieved":[198],"between":[199,490],"another":[203],"similar":[204],"one.":[205],"Protein":[206],"matrices,":[207,475],"on":[208,274,301,376,507],"hand,":[211],"offer":[212],"greater":[214,306,319,340],"breadth":[215],"calculation":[217],"not":[219,545],"five":[223],"times":[224],"many":[226,448],"common":[227,246,351,436],"amino":[228],"acid":[229],"residues":[230,380],"DNA":[234],"bases,":[235],"they":[236],"incorporate":[237],"significant":[239],"amount":[240],"evolutionary":[242,342,488],"information.":[243],"matrices":[247,367,412],"here":[248],"position":[251],"accepted":[252,276,323],"mutation":[253],"(PAM)":[254],"[1,":[255],"2]":[256],"BLOSUM":[258,366,411,442,474,483],"[3]":[259],"tables.":[261],"first":[263,303],"PAM":[264,285,292,315,353],"was":[266],"late":[270],"1970s":[271],"relied":[273,375],"noting":[275],"residue":[277,521],"substitutions":[278],"protein":[280,449],"sequences":[281,510],"produce":[283],"1":[286],"table.":[287],"Subsequent":[288],"tables":[289],"family":[293,409],"by":[297],"multiplication":[298],"models":[299],"based":[300,506],"matrix.":[304,393,433,468],"multiplication,":[308],"higher":[310,477],"number":[312,321,479],"series":[316],"mutations":[324],"involved":[328],"proteins":[331,360,389],"create":[334,391,431],"tables,":[336],"thus":[338],"divergence":[343,489],"those":[345],"proteins.":[346],"One":[347],"matrices\u2014the":[352],"250":[354],"matrix\u2014":[355],"represents":[356],"subset":[358],"approximately":[362],"80%":[363],"diversity.":[364],"were":[368,461],"early":[372],"90s":[373],"presence":[378],"blocks":[383,395],"conserved":[385],"regions":[386],"related":[388],"These":[394,418],"accessed":[398],"BLOCKS":[401,428,455],"[4,":[402],"5]":[403],"database.":[404],"There":[405],"differentiated":[415],"numbers.":[417],"numbers,":[419],"however,":[420],"represent":[421],"minimum":[423],"percentage":[424],"set":[440],"62,":[443],"default":[445],"setting":[446],"applications.":[451],"It":[452],"indicates":[453],"at":[457],"least":[458],"62%":[459],"creation":[465],"connected":[480],"matrix,":[484],"smaller":[486],"sequences.":[491],"Once":[492],"established,":[498],"computer":[500,527],"make":[502],"own":[504],"two":[509],"aligned\u2014inserting":[513],"\u2018score\u2019":[515],"each":[517,530],"base":[519],"alignment.":[522],"However,":[523],"allow":[525],"select":[533],"match\u2014or":[536],"run":[537],"matches\u2014that":[539],"gives":[540],"would":[544],"necessarily":[546],"yield":[547],"best":[549],"ignores":[553],"biological":[554],"insertions":[555]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":4},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":3}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}