{"id":"https://openalex.org/W2164455317","doi":"https://doi.org/10.1093/bioinformatics/btt694","title":"Revisiting amino acid substitution matrices for identifying distantly related proteins","display_name":"Revisiting amino acid substitution matrices for identifying distantly related proteins","publication_year":2013,"publication_date":"2013-11-26","ids":{"openalex":"https://openalex.org/W2164455317","doi":"https://doi.org/10.1093/bioinformatics/btt694","mag":"2164455317","pmid":"https://pubmed.ncbi.nlm.nih.gov/24281694"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btt694","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt694","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/30/3/317/48915258/bioinformatics_30_3_317.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/30/3/317/48915258/bioinformatics_30_3_317.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5113709326","display_name":"K Yamada","orcid":null},"institutions":[{"id":"https://openalex.org/I73613424","display_name":"National Institute of Advanced Industrial Science and Technology","ror":"https://ror.org/01703db54","country_code":"JP","type":"government","lineage":["https://openalex.org/I73613424"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Kazunori Yamada","raw_affiliation_strings":["Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan","institution_ids":["https://openalex.org/I73613424"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5074475230","display_name":"Kentaro Tomii","orcid":"https://orcid.org/0000-0002-4567-4768"},"institutions":[{"id":"https://openalex.org/I73613424","display_name":"National Institute of Advanced Industrial Science and Technology","ror":"https://ror.org/01703db54","country_code":"JP","type":"government","lineage":["https://openalex.org/I73613424"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Kentaro Tomii","raw_affiliation_strings":["Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan","institution_ids":["https://openalex.org/I73613424"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5074475230"],"corresponding_institution_ids":["https://openalex.org/I73613424"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":{"value":3989,"currency":"USD","value_usd":3989},"fwci":1.945,"has_fulltext":true,"cited_by_count":53,"citation_normalized_percentile":{"value":0.86392904,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":88,"max":99},"biblio":{"volume":"30","issue":"3","first_page":"317","last_page":"325"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.6204000115394592,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.6204000115394592,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.17550000548362732,"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/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.04529999941587448,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/substitution","display_name":"Substitution (logic)","score":0.7668871283531189},{"id":"https://openalex.org/keywords/amino-acid-substitution","display_name":"Amino acid substitution","score":0.6588761210441589},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5016970634460449},{"id":"https://openalex.org/keywords/amino-acid","display_name":"Amino acid","score":0.4710618853569031},{"id":"https://openalex.org/keywords/protein-evolution","display_name":"Protein evolution","score":0.4290462136268616},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4128398895263672},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.3766636848449707},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.3492574095726013},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.32291680574417114},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3195589780807495},{"id":"https://openalex.org/keywords/mutation","display_name":"Mutation","score":0.16704785823822021},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1273845136165619},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.12121105194091797}],"concepts":[{"id":"https://openalex.org/C2778220771","wikidata":"https://www.wikidata.org/wiki/Q1522579","display_name":"Substitution (logic)","level":2,"score":0.7668871283531189},{"id":"https://openalex.org/C2993683473","wikidata":"https://www.wikidata.org/wiki/Q30693176","display_name":"Amino acid substitution","level":4,"score":0.6588761210441589},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5016970634460449},{"id":"https://openalex.org/C515207424","wikidata":"https://www.wikidata.org/wiki/Q8066","display_name":"Amino acid","level":2,"score":0.4710618853569031},{"id":"https://openalex.org/C2992240565","wikidata":"https://www.wikidata.org/wiki/Q856529","display_name":"Protein evolution","level":3,"score":0.4290462136268616},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4128398895263672},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3766636848449707},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.3492574095726013},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.32291680574417114},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3195589780807495},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.16704785823822021},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1273845136165619},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.12121105194091797}],"mesh":[{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","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":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","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":true},{"descriptor_ui":"D017386","descriptor_name":"Sequence Homology, Amino Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017386","descriptor_name":"Sequence Homology, Amino Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019943","descriptor_name":"Amino Acid Substitution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019943","descriptor_name":"Amino Acid Substitution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019943","descriptor_name":"Amino Acid Substitution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D025341","descriptor_name":"Principal Component Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D025341","descriptor_name":"Principal Component Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D025341","descriptor_name":"Principal Component Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btt694","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt694","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/30/3/317/48915258/bioinformatics_30_3_317.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:24281694","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24281694","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":"Bioinformatics (Oxford, England)","raw_type":"Journal Article"},{"id":"pmh:oai:europepmc.org:2888625","is_oa":false,"landing_page_url":"http://europepmc.org/articles/PMC3904525","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:3904525","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3904525","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btt694","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt694","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/30/3/317/48915258/bioinformatics_30_3_317.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320320912","display_name":"Ministry of Education, Culture, Sports, Science and Technology","ror":"https://ror.org/048rj2z13"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2164455317.pdf","grobid_xml":"https://content.openalex.org/works/W2164455317.grobid-xml"},"referenced_works_count":46,"referenced_works":["https://openalex.org/W21816278","https://openalex.org/W1500214331","https://openalex.org/W1526255571","https://openalex.org/W1596429464","https://openalex.org/W1971048099","https://openalex.org/W1978594833","https://openalex.org/W1978667203","https://openalex.org/W1995513161","https://openalex.org/W2010026647","https://openalex.org/W2027122912","https://openalex.org/W2028769673","https://openalex.org/W2033177501","https://openalex.org/W2036149515","https://openalex.org/W2043046527","https://openalex.org/W2061567716","https://openalex.org/W2067852761","https://openalex.org/W2084787613","https://openalex.org/W2089499735","https://openalex.org/W2093946436","https://openalex.org/W2097289634","https://openalex.org/W2097818324","https://openalex.org/W2099946731","https://openalex.org/W2101335101","https://openalex.org/W2102124048","https://openalex.org/W2115399262","https://openalex.org/W2118475569","https://openalex.org/W2118601726","https://openalex.org/W2122987904","https://openalex.org/W2128653811","https://openalex.org/W2133312664","https://openalex.org/W2133657429","https://openalex.org/W2137690161","https://openalex.org/W2137955461","https://openalex.org/W2139154175","https://openalex.org/W2140187548","https://openalex.org/W2140745046","https://openalex.org/W2143210482","https://openalex.org/W2147817822","https://openalex.org/W2150582264","https://openalex.org/W2157809793","https://openalex.org/W2158714788","https://openalex.org/W2163694519","https://openalex.org/W2164260969","https://openalex.org/W2170747616","https://openalex.org/W2582743722","https://openalex.org/W6681795929"],"related_works":["https://openalex.org/W4255149369","https://openalex.org/W2622907957","https://openalex.org/W3186625252","https://openalex.org/W2899747918","https://openalex.org/W2331216766","https://openalex.org/W2089387174","https://openalex.org/W1926060057","https://openalex.org/W1566785938","https://openalex.org/W2143210482","https://openalex.org/W1770919676"],"abstract_inverted_index":{"MOTIVATION:":[0],"Although":[1],"many":[2],"amino":[3,138,183],"acid":[4,139,184],"substitution":[5],"matrices":[6,58,86,110,148,185,214],"have":[7],"been":[8,13],"developed,":[9],"it":[10,37],"has":[11],"not":[12],"well":[14],"understood":[15],"which":[16,66,129,151],"is":[17,76,100],"the":[18,108,117,144,162,178],"best":[19],"for":[20,24,93,218],"similarity":[21,133,195],"searches,":[22],"especially":[23],"remote":[25,47,105],"homology":[26,48,106],"detection.":[27],"Therefore,":[28],"we":[29,61,67],"collected":[30],"information":[31],"related":[32],"to":[33,102,125,173],"existing":[34,57,83,109,163],"matrices,":[35],"condensed":[36],"and":[38,59,78,149,166,201,215],"derived":[39],"a":[40,63,131],"novel":[41,64,132],"matrix":[42,122,164],"that":[43,81,98,126,153,160],"can":[44,205],"detect":[45,103],"more":[46,104],"than":[49,107,159],"ever.":[50],"RESULTS:":[51],"Using":[52],"principal":[53],"component":[54],"analysis":[55],"with":[56,80,89,136,161,190],"benchmarks,":[60],"developed":[62,121,192,213],"matrix,":[65,193],"designate":[68],"as":[69,199],"MIQS.":[70],"The":[71],"detection":[72],"performance":[73,118],"of":[74,82,119,127,147,177,182],"MIQS":[75,99,154],"validated":[77],"compared":[79],"general":[84],"purpose":[85],"using":[87],"SSEARCH":[88],"optimized":[90],"gap":[91],"penalties":[92],"each":[94],"matrix.":[95,140],"Results":[96],"show":[97],"able":[101],"on":[111],"an":[112],"independent":[113],"dataset.":[114],"In":[115],"addition,":[116],"our":[120,191],"was":[123,130],"superior":[124],"CS-BLAST,":[128],"search":[134,196],"method":[135],"no":[137],"We":[141],"also":[142],"evaluated":[143],"alignment":[145,157],"quality":[146],"methods,":[150],"revealed":[152],"shows":[155],"higher":[156],"sensitivity":[158],"series":[165],"CS-BLAST.":[167],"Fundamentally,":[168],"these":[169],"results":[170],"are":[171,221],"expected":[172],"constitute":[174],"good":[175],"proof":[176],"availability":[179],"and/or":[180],"importance":[181],"in":[186],"sequence":[187],"analysis.":[188],"Moreover,":[189],"sophisticated":[194],"methods":[197,204],"such":[198],"sequence-profile":[200],"profile-profile":[202],"comparison":[203],"be":[206],"improved":[207],"further.":[208],"AVAILABILITY":[209],"AND":[210],"IMPLEMENTATION:":[211],"Newly":[212],"datasets":[216],"used":[217],"this":[219],"study":[220],"available":[222],"at":[223],"http://csas.cbrc.jp/Ssearch/.":[224]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":4},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":11},{"year":2016,"cited_by_count":8},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":3}],"updated_date":"2026-08-27T14:10:00.468798","created_date":"2025-10-10T00:00:00"}
