{"id":"https://openalex.org/W2051151530","doi":"https://doi.org/10.1002/(sici)1097-0134(19980701)32:1<88::aid-prot10>3.0.co;2-j","title":"Generalized affine gap costs for protein sequence alignment","display_name":"Generalized affine gap costs for protein sequence alignment","publication_year":1998,"publication_date":"1998-07-01","ids":{"openalex":"https://openalex.org/W2051151530","doi":"https://doi.org/10.1002/(sici)1097-0134(19980701)32:1<88::aid-prot10>3.0.co;2-j","mag":"2051151530","pmid":"https://pubmed.ncbi.nlm.nih.gov/9672045"},"language":"en","primary_location":{"id":"doi:10.1002/(sici)1097-0134(19980701)32:1<88::aid-prot10>3.0.co;2-j","doi":"https://doi.org/10.1002/(sici)1097-0134(19980701)32:1<88::aid-prot10>3.0.co;2-j","is_oa":false,"landing_page_url":"https://doi.org/10.1002/(sici)1097-0134(19980701)32:1<88::aid-prot10>3.0.co;2-j","pdf_url":null,"source":{"id":"https://openalex.org/S121161810","display_name":"Proteins Structure Function and Bioinformatics","issn_l":"0887-3585","issn":["0887-3585","1097-0134"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-c","doyens","jufo-1","ki-jl-1","medline","norway-1","poland-100","russia-white-list-2"],"host_organization":"https://openalex.org/P4310320595","host_organization_name":"Wiley","host_organization_lineage":["https://openalex.org/P4310320595"],"host_organization_lineage_names":["Wiley"],"type":"journal"},"license":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proteins: Structure, Function, and Genetics","raw_type":"journal-article"},"volume":null,"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/A5015061000","display_name":"Stephen F. Altschul","orcid":"https://orcid.org/0000-0003-2120-9631","observed_orcids":["https://orcid.org/0000-0003-2120-9631"]},"institutions":[{"id":"https://openalex.org/I1299303238","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]},{"id":"https://openalex.org/I4210109390","display_name":"National Center for Biotechnology Information","ror":"https://ror.org/02meqm098","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I2800548410","https://openalex.org/I4210109390"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Stephen F. Altschul","raw_affiliation_strings":["National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland","National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland","institution_ids":["https://openalex.org/I1299303238","https://openalex.org/I4210109390"]},{"raw_affiliation_string":"National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894","institution_ids":["https://openalex.org/I1299303238","https://openalex.org/I4210109390"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5015061000"],"corresponding_institution_ids":["https://openalex.org/I1299303238","https://openalex.org/I4210109390"],"apc_list":{"value":4550,"currency":"USD","value_usd":4550},"apc_paid":null,"fwci":0.8812,"has_fulltext":false,"cited_by_count":75,"citation_normalized_percentile":{"value":0.71156255,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":88,"max":98},"biblio":{"volume":"32","issue":"1","first_page":"88","last_page":"96"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9164999723434448,"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":0.9164999723434448,"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":0.03400000184774399,"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/T12946","display_name":"Fractal and DNA sequence analysis","score":0.029400000348687172,"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/protein-sequence-alignment","display_name":"protein sequence alignment","score":0.9990000128746033},{"id":"https://openalex.org/keywords/local-sequence-alignment","display_name":"local alignment","score":0.7310000061988831},{"id":"https://openalex.org/keywords/extreme-value-distribution","display_name":"extreme value distribution","score":0.9150000214576721},{"id":"https://openalex.org/keywords/multiple-sequence-alignment","display_name":"multiple sequence alignment","score":0.5350000262260437},{"id":"https://openalex.org/keywords/distantly-related-proteins","display_name":"distantly related proteins","score":0.7409999966621399},{"id":"https://openalex.org/keywords/conserved-residues","display_name":"conserved residues","score":0.652999997138977},{"id":"https://openalex.org/keywords/alignment-scoring","display_name":"alignment scoring","score":0.34700000286102295}],"concepts":[{"id":"https://openalex.org/C92757383","wikidata":"https://www.wikidata.org/wiki/Q382497","display_name":"Affine transformation","level":2,"score":0.8472208380699158},{"id":"https://openalex.org/C177148314","wikidata":"https://www.wikidata.org/wiki/Q170084","display_name":"Generalization","level":2,"score":0.7871732711791992},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5926083326339722},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4902103543281555},{"id":"https://openalex.org/C88031987","wikidata":"https://www.wikidata.org/wiki/Q1377767","display_name":"Multiple sequence alignment","level":5,"score":0.4697421193122864},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.4540104269981384},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4340667426586151},{"id":"https://openalex.org/C110121322","wikidata":"https://www.wikidata.org/wiki/Q865811","display_name":"Distribution (mathematics)","level":2,"score":0.42745670676231384},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.3918894827365875},{"id":"https://openalex.org/C126255220","wikidata":"https://www.wikidata.org/wiki/Q141495","display_name":"Mathematical optimization","level":1,"score":0.36145544052124023},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.15633517503738403},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.152236670255661},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.15162095427513123},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.11612722277641296},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.11447611451148987},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1002/(sici)1097-0134(19980701)32:1<88::aid-prot10>3.0.co;2-j","doi":"https://doi.org/10.1002/(sici)1097-0134(19980701)32:1<88::aid-prot10>3.0.co;2-j","is_oa":false,"landing_page_url":"https://doi.org/10.1002/(sici)1097-0134(19980701)32:1<88::aid-prot10>3.0.co;2-j","pdf_url":null,"source":{"id":"https://openalex.org/S121161810","display_name":"Proteins Structure Function and Bioinformatics","issn_l":"0887-3585","issn":["0887-3585","1097-0134"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-c","doyens","jufo-1","ki-jl-1","medline","norway-1","poland-100","russia-white-list-2"],"host_organization":"https://openalex.org/P4310320595","host_organization_name":"Wiley","host_organization_lineage":["https://openalex.org/P4310320595"],"host_organization_lineage_names":["Wiley"],"type":"journal"},"license":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proteins: Structure, Function, and Genetics","raw_type":"journal-article"},{"id":"doi:10.1002/(sici)1097-0134(19980701)32:1<88::aid-prot10>3.3.co;2-x","doi":"https://doi.org/10.1002/(sici)1097-0134(19980701)32:1<88::aid-prot10>3.3.co;2-x","is_oa":false,"landing_page_url":"https://doi.org/10.1002/(sici)1097-0134(19980701)32:1<88::aid-prot10>3.3.co;2-x","pdf_url":null,"source":{"id":"https://openalex.org/S121161810","display_name":"Proteins Structure Function and Bioinformatics","issn_l":"0887-3585","issn":["0887-3585","1097-0134"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-c","doyens","jufo-1","ki-jl-1","medline","norway-1","poland-100","russia-white-list-2"],"host_organization":"https://openalex.org/P4310320595","host_organization_name":"Wiley","host_organization_lineage":["https://openalex.org/P4310320595"],"host_organization_lineage_names":["Wiley"],"type":"journal"},"license":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proteins: Structure, Function, and Genetics","raw_type":"journal-article"},{"id":"pmid:9672045","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/9672045","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,"listed_in":[],"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":"Proteins","raw_type":"Journal Article"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.453.8029","doi":null,"is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.453.8029","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://brendelgroup.org/WikiVB/data/media/_SCRATCH/cmsORIG/proteins32-88.pdf","raw_type":"text"}],"best_oa_location":null,"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":69,"referenced_works":["https://openalex.org/W1003773566","https://openalex.org/W1481346850","https://openalex.org/W1502621331","https://openalex.org/W1527979595","https://openalex.org/W1605425227","https://openalex.org/W1659313070","https://openalex.org/W1768635289","https://openalex.org/W1965998064","https://openalex.org/W1969153299","https://openalex.org/W1969850472","https://openalex.org/W1971143006","https://openalex.org/W1973578915","https://openalex.org/W1977618577","https://openalex.org/W1982496832","https://openalex.org/W1983265703","https://openalex.org/W1983698816","https://openalex.org/W1985618229","https://openalex.org/W1988670311","https://openalex.org/W1994414218","https://openalex.org/W1996897910","https://openalex.org/W1998008917","https://openalex.org/W1998300401","https://openalex.org/W2000758249","https://openalex.org/W2005726782","https://openalex.org/W2008120462","https://openalex.org/W2011820950","https://openalex.org/W2013570924","https://openalex.org/W2014660704","https://openalex.org/W2015292449","https://openalex.org/W2018885841","https://openalex.org/W2022368654","https://openalex.org/W2026257220","https://openalex.org/W2029372233","https://openalex.org/W2032295681","https://openalex.org/W2034767282","https://openalex.org/W2041966417","https://openalex.org/W2041976742","https://openalex.org/W2044966609","https://openalex.org/W2045067706","https://openalex.org/W2045100386","https://openalex.org/W2048102092","https://openalex.org/W2048869777","https://openalex.org/W2054600139","https://openalex.org/W2055043387","https://openalex.org/W2061833373","https://openalex.org/W2068176376","https://openalex.org/W2068448872","https://openalex.org/W2074231493","https://openalex.org/W2076540369","https://openalex.org/W2076911571","https://openalex.org/W2082658158","https://openalex.org/W2085668020","https://openalex.org/W2087064593","https://openalex.org/W2094519647","https://openalex.org/W2102122585","https://openalex.org/W2105516199","https://openalex.org/W2108215151","https://openalex.org/W2109465247","https://openalex.org/W2129361631","https://openalex.org/W2135326109","https://openalex.org/W2136739161","https://openalex.org/W2143210482","https://openalex.org/W2149208773","https://openalex.org/W2156179961","https://openalex.org/W2158714788","https://openalex.org/W2312194337","https://openalex.org/W2432429035","https://openalex.org/W4236611442","https://openalex.org/W4239620712"],"related_works":["https://openalex.org/W7100973223","https://openalex.org/W2171280596","https://openalex.org/W1533639216","https://openalex.org/W6939282607","https://openalex.org/W4255325480","https://openalex.org/W2172163287","https://openalex.org/W1994211569","https://openalex.org/W2008120462","https://openalex.org/W1983265703","https://openalex.org/W1659313070"],"abstract_inverted_index":{"Based":[0],"on":[1],"the":[2,25,118],"observation":[3],"that":[4,48,76],"a":[5,22,28,31,67],"single":[6],"mutational":[7],"event":[8],"can":[9],"delete":[10],"or":[11,37],"insert":[12],"multiple":[13,38,143],"residues,":[14],"affine":[15,71,111,132],"gap":[16,72,94,112,133],"costs":[17,73,95,113,134],"for":[18,24,108,129],"sequence":[19],"alignment":[20,126],"charge":[21],"penalty":[23],"existence":[26],"of":[27,40,64,70,86,121,125],"gap,":[29],"and":[30,124],"further":[32],"length-dependent":[33],"penalty.":[34],"From":[35],"structural":[36],"alignments":[39,90,116],"distantly":[41],"related":[42],"proteins,":[43],"it":[44],"has":[45],"been":[46],"observed":[47],"conserved":[49],"residues":[50],"frequently":[51],"fall":[52],"into":[53],"ungapped":[54],"blocks":[55],"separated":[56],"by":[57],"relatively":[58],"nonconserved":[59,78],"regions.":[60],"To":[61],"take":[62],"advantage":[63],"this":[65],"structure,":[66],"simple":[68],"generalization":[69],"is":[74,96,138],"proposed":[75],"allows":[77],"regions":[79],"to":[80,99,142],"be":[81],"effectively":[82],"ignored.":[83],"The":[84],"distribution":[85],"scores":[87],"from":[88,117],"local":[89],"using":[91],"these":[92],"generalized":[93,110,131],"shown":[97],"empirically":[98],"follow":[100],"an":[101],"extreme":[102],"value":[103],"distribution.":[104],"Examples":[105],"are":[106,135],"presented":[107],"which":[109],"yield":[114],"superior":[115],"standpoints":[119],"both":[120],"statistical":[122],"significance":[123],"accuracy.":[127],"Guidelines":[128],"selecting":[130],"discussed,":[136],"as":[137],"their":[139],"possible":[140],"application":[141],"alignment.":[144]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":2},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":4},{"year":2014,"cited_by_count":3},{"year":2013,"cited_by_count":4}],"updated_date":"2026-11-04T10:54:05.112534","created_date":"2016-06-24T00:00:00"}
