{"id":"https://openalex.org/W2532368742","doi":"https://doi.org/10.1093/nar/gkw934","title":"ATGC database and ATGC-COGs: an updated resource for micro- and macro-evolutionary studies of prokaryotic genomes and protein family annotation","display_name":"ATGC database and ATGC-COGs: an updated resource for micro- and macro-evolutionary studies of prokaryotic genomes and protein family annotation","publication_year":2016,"publication_date":"2016-10-12","ids":{"openalex":"https://openalex.org/W2532368742","doi":"https://doi.org/10.1093/nar/gkw934","mag":"2532368742","pmid":"https://pubmed.ncbi.nlm.nih.gov/28053163"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkw934","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkw934","pdf_url":"https://academic.oup.com/nar/article-pdf/45/D1/D210/8847209/gkw934.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/nar/article-pdf/45/D1/D210/8847209/gkw934.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5042113315","display_name":"David M. Kristensen","orcid":"https://orcid.org/0000-0003-0657-1632"},"institutions":[{"id":"https://openalex.org/I126307644","display_name":"University of Iowa","ror":"https://ror.org/036jqmy94","country_code":"US","type":"education","lineage":["https://openalex.org/I126307644"]},{"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":"David M. Kristensen","raw_affiliation_strings":["Department of Biomedical Engineering, University of Iowa, Iowa City, IA 52242, USA david-kristensen@uiowa.edu","National Center for Biotechnology Information, National Library of Medicine, National Institute of Health, Bethesda, MD 20894, USA","Department of Biomedical Engineering, University of Iowa, Iowa City, IA 52242, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Engineering, University of Iowa, Iowa City, IA 52242, USA david-kristensen@uiowa.edu","institution_ids":["https://openalex.org/I126307644"]},{"raw_affiliation_string":"National Center for Biotechnology Information, National Library of Medicine, National Institute of Health, Bethesda, MD 20894, USA","institution_ids":["https://openalex.org/I4210109390"]},{"raw_affiliation_string":"Department of Biomedical Engineering, University of Iowa, Iowa City, IA 52242, USA","institution_ids":["https://openalex.org/I126307644"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012792532","display_name":"Yuri I. Wolf","orcid":"https://orcid.org/0000-0002-0247-8708"},"institutions":[{"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":false,"raw_author_name":"Yuri I. Wolf","raw_affiliation_strings":["National Center for Biotechnology Information, National Library of Medicine, National Institute of Health, Bethesda, MD 20894, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Center for Biotechnology Information, National Library of Medicine, National Institute of Health, Bethesda, MD 20894, USA","institution_ids":["https://openalex.org/I4210109390"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5035240489","display_name":"Eugene V. Koonin","orcid":"https://orcid.org/0000-0003-3943-8299"},"institutions":[{"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":false,"raw_author_name":"Eugene V. Koonin","raw_affiliation_strings":["National Center for Biotechnology Information, National Library of Medicine, National Institute of Health, Bethesda, MD 20894, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Center for Biotechnology Information, National Library of Medicine, National Institute of Health, Bethesda, MD 20894, USA","institution_ids":["https://openalex.org/I4210109390"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5042113315"],"corresponding_institution_ids":["https://openalex.org/I126307644","https://openalex.org/I4210109390"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":3.6557,"has_fulltext":false,"cited_by_count":51,"citation_normalized_percentile":{"value":0.93336768,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"45","issue":"D1","first_page":"D210","last_page":"D218"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9998999834060669,"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":0.9998999834060669,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9900000095367432,"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/T11791","display_name":"Microbial Community Ecology and Physiology","score":0.9837999939918518,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/refseq","display_name":"RefSeq","score":0.9484584331512451},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.7620865106582642},{"id":"https://openalex.org/keywords/synteny","display_name":"Synteny","score":0.7256709933280945},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.7089711427688599},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.5789134502410889},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.496811181306839},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.47329941391944885},{"id":"https://openalex.org/keywords/phylogenetics","display_name":"Phylogenetics","score":0.4231521189212799},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.39917609095573425},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3929813802242279},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.364774227142334},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.10908398032188416}],"concepts":[{"id":"https://openalex.org/C151810110","wikidata":"https://www.wikidata.org/wiki/Q7307074","display_name":"RefSeq","level":4,"score":0.9484584331512451},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.7620865106582642},{"id":"https://openalex.org/C53702515","wikidata":"https://www.wikidata.org/wiki/Q971246","display_name":"Synteny","level":4,"score":0.7256709933280945},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.7089711427688599},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.5789134502410889},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.496811181306839},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.47329941391944885},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.4231521189212799},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.39917609095573425},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3929813802242279},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.364774227142334},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.10908398032188416}],"mesh":[{"descriptor_ui":"D011387","descriptor_name":"Prokaryotic Cells","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011387","descriptor_name":"Prokaryotic Cells","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011387","descriptor_name":"Prokaryotic Cells","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"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":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064878","descriptor_name":"Web Browser","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D064878","descriptor_name":"Web Browser","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D064878","descriptor_name":"Web Browser","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/nar/gkw934","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkw934","pdf_url":"https://academic.oup.com/nar/article-pdf/45/D1/D210/8847209/gkw934.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:28053163","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28053163","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":"Nucleic acids research","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:5210634","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5210634","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":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Res","raw_type":"Text"},{"id":"pmh:oai:open-archive.highwire.org:nar:45/D1/D210","is_oa":false,"landing_page_url":"http://nar.oxfordjournals.org/cgi/content/short/45/D1/D210","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"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"}],"best_oa_location":{"id":"doi:10.1093/nar/gkw934","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkw934","pdf_url":"https://academic.oup.com/nar/article-pdf/45/D1/D210/8847209/gkw934.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":41,"referenced_works":["https://openalex.org/W1519820746","https://openalex.org/W1968828904","https://openalex.org/W1970764623","https://openalex.org/W1972595484","https://openalex.org/W1990453950","https://openalex.org/W1992159722","https://openalex.org/W1997401091","https://openalex.org/W2009234149","https://openalex.org/W2019216543","https://openalex.org/W2031611770","https://openalex.org/W2033718613","https://openalex.org/W2045246328","https://openalex.org/W2056251063","https://openalex.org/W2064415648","https://openalex.org/W2095627741","https://openalex.org/W2099321785","https://openalex.org/W2118077323","https://openalex.org/W2119632499","https://openalex.org/W2124351063","https://openalex.org/W2129081404","https://openalex.org/W2129452435","https://openalex.org/W2131730777","https://openalex.org/W2133031372","https://openalex.org/W2133793243","https://openalex.org/W2136632285","https://openalex.org/W2143335572","https://openalex.org/W2144368480","https://openalex.org/W2144377764","https://openalex.org/W2145100181","https://openalex.org/W2149887988","https://openalex.org/W2152179349","https://openalex.org/W2155606054","https://openalex.org/W2158714788","https://openalex.org/W2164898486","https://openalex.org/W2168048337","https://openalex.org/W2169235657","https://openalex.org/W2173732482","https://openalex.org/W2214414678","https://openalex.org/W2336330109","https://openalex.org/W2340958225","https://openalex.org/W6655062678"],"related_works":["https://openalex.org/W2116418175","https://openalex.org/W2174809885","https://openalex.org/W2883025420","https://openalex.org/W2057191541","https://openalex.org/W2949296710","https://openalex.org/W1992658754","https://openalex.org/W2111939425","https://openalex.org/W2065083790","https://openalex.org/W2604174992","https://openalex.org/W2375383082"],"abstract_inverted_index":{"The":[0,99,191],"Alignable":[1],"Tight":[2],"Genomic":[3],"Clusters":[4],"(ATGCs)":[5],"database":[6,101,144,193],"is":[7,33,73,94,171,194],"a":[8,34,50,59,81,118,159],"collection":[9,91],"of":[10,37,49,53,62,77,84,92,105,112,120,128,134,151,156,166,186,200],"closely":[11],"related":[12],"bacterial":[13],"and":[14,58,178,204],"archaeal":[15],"genomes":[16,43,152],"that":[17,44],"provides":[18],"several":[19,146],"tools":[20],"to":[21],"aid":[22],"research":[23],"into":[24,154],"evolutionary":[25],"processes":[26],"in":[27,65,108],"the":[28,46,66,89,124,131,135,142,163,167,187,198,205],"microbial":[29],"world.":[30],"Each":[31],"ATGC":[32,72,100,143,168,192],"taxonomy-independent":[35],"cluster":[36],"2":[38],"or":[39],"more":[40],"completely":[41,175],"sequenced":[42],"meet":[45],"objective":[47],"criteria":[48],"high":[51],"degree":[52],"local":[54],"gene":[55],"order":[56],"(synteny)":[57],"small":[60],"number":[61],"synonymous":[63],"substitutions":[64],"protein-coding":[67],"genes.":[68],"As":[69],"such,":[70],"each":[71,129,138],"suited":[74],"for":[75,96],"analysis":[76],"microevolutionary":[78],"variations":[79],"within":[80,137],"cohesive":[82],"group":[83],"organisms":[85,136],"(e.g.":[86],"species),":[87],"whereas":[88],"entire":[90],"ATGCs":[93],"useful":[95],"macroevolutionary":[97],"studies.":[98],"includes":[102],"many":[103],"forms":[104],"pre-computed":[106],"data,":[107],"particular":[109],"ATGC-COGs":[110],"(Clusters":[111],"Orthologous":[113],"Genes),":[114],"multiple":[115],"sequence":[116],"alignments,":[117],"set":[119],"'index'":[121],"orthologs":[122],"representing":[123],"most":[125],"well-conserved":[126],"members":[127],"ATGC-COG,":[130],"phylogenetic":[132],"tree":[133],"ATGC,":[139],"etc.":[140],"Although":[141],"contains":[145],"million":[147],"proteins":[148],"from":[149],"thousands":[150],"organized":[153],"hundreds":[155],"clusters":[157],"(roughly":[158],"4-fold":[160],"increase":[161],"since":[162],"last":[164],"version":[165],"database),":[169],"it":[170],"now":[172],"built":[173],"with":[174],"automated":[176],"methods":[177],"will":[179],"be":[180],"regularly":[181],"updated":[182],"following":[183],"new":[184],"releases":[185],"NCBI":[188,206],"RefSeq":[189],"database.":[190],"hosted":[195],"jointly":[196],"at":[197,202,207],"University":[199],"Iowa":[201],"dmk-brain.ecn.uiowa.edu/ATGC/":[203],"ftp.ncbi.nlm.nih.gov/pub/kristensen/ATGC/atgc_home.html.":[208]},"counts_by_year":[{"year":2025,"cited_by_count":7},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":5},{"year":2020,"cited_by_count":7},{"year":2019,"cited_by_count":9},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":7}],"updated_date":"2026-05-19T21:40:30.786675","created_date":"2025-10-10T00:00:00"}
