{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,7]],"date-time":"2026-02-07T21:22:40Z","timestamp":1770499360674,"version":"3.49.0"},"reference-count":19,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2016,10,4]],"date-time":"2016-10-04T00:00:00Z","timestamp":1475539200000},"content-version":"vor","delay-in-days":1235,"URL":"http:\/\/creativecommons.org\/licenses\/by\/3.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,7,1]]},"DOI":"10.1093\/nar\/gkt399","type":"journal-article","created":{"date-parts":[[2013,5,18]],"date-time":"2013-05-18T20:55:26Z","timestamp":1368910526000},"page":"W242-W248","source":"Crossref","is-referenced-by-count":22,"title":["The PhyloFacts FAT-CAT web server: ortholog identification and function prediction using fast approximate tree classification"],"prefix":"10.1093","volume":"41","author":[{"given":"Cyrus","family":"Afrasiabi","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bushra","family":"Samad","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"David","family":"Dineen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Christopher","family":"Meacham","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kimmen","family":"Sj\u00f6lander","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2013,5,18]]},"reference":[{"key":"key\n\t\t\t\t20171013134712_gkt399-B1","doi-asserted-by":"crossref","first-page":"R83","DOI":"10.1186\/gb-2006-7-9-r83","article-title":"PhyloFacts: an online structural phylogenomic encyclopedia for protein functional and structural classification","volume":"7","author":"Krishnamurthy","year":"2006","journal-title":"Genome Biol."},{"key":"key\n\t\t\t\t20171013134712_gkt399-B2","doi-asserted-by":"crossref","first-page":"D138","DOI":"10.1093\/nar\/gkh121","article-title":"The Pfam protein families database","volume":"32","author":"Bateman","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20171013134712_gkt399-B3","doi-asserted-by":"crossref","first-page":"e9490","DOI":"10.1371\/journal.pone.0009490","article-title":"FastTree 2\u2014approximately maximum-likelihood trees for large alignments","volume":"5","author":"Price","year":"2010","journal-title":"PLoS One"},{"key":"key\n\t\t\t\t20171013134712_gkt399-B4","doi-asserted-by":"crossref","first-page":"S12","DOI":"10.1186\/1471-2148-7-S1-S12","article-title":"FlowerPower: clustering proteins into domain architecture classes for phylogenomic inference of protein function","volume":"7","author":"Krishnamurthy","year":"2007","journal-title":"BMC Evol. Biol."},{"key":"key\n\t\t\t\t20171013134712_gkt399-B5","doi-asserted-by":"crossref","first-page":"e160","DOI":"10.1371\/journal.pcbi.0030160","article-title":"Automated protein subfamily identification and classification","volume":"3","author":"Brown","year":"2007","journal-title":"PLoS Comput. Biol."},{"key":"key\n\t\t\t\t20171013134712_gkt399-B6","doi-asserted-by":"crossref","first-page":"413","DOI":"10.1093\/bib\/bbr036","article-title":"Ortholog identification in the presence of domain architecture rearrangement","volume":"12","author":"Sj\u00f6lander","year":"2011","journal-title":"Brief. Bioinformatics"},{"key":"key\n\t\t\t\t20171013134712_gkt399-B7","doi-asserted-by":"crossref","first-page":"W84","DOI":"10.1093\/nar\/gkp373","article-title":"Berkeley PHOG: PhyloFacts orthology group prediction web server","volume":"37","author":"Datta","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20171013134712_gkt399-B8","doi-asserted-by":"crossref","first-page":"D289","DOI":"10.1093\/nar\/gkq1238","article-title":"OMA 2011: orthology inference among 1000 complete genomes","volume":"39","author":"Altenhoff","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20171013134712_gkt399-B9","doi-asserted-by":"crossref","first-page":"D363","DOI":"10.1093\/nar\/gkj123","article-title":"OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups","volume":"34","author":"Chen","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20171013134712_gkt399-B10","doi-asserted-by":"crossref","first-page":"14","DOI":"10.1186\/1471-2105-3-14","article-title":"RIO: analyzing proteomes by automated phylogenomics using resampled inference of orthologs","volume":"3","author":"Zmasek","year":"2002","journal-title":"BMC Bioinformatics"},{"key":"key\n\t\t\t\t20171013134712_gkt399-B11","doi-asserted-by":"crossref","first-page":"D196","DOI":"10.1093\/nar\/gkp931","article-title":"InParanoid 7: new algorithms and tools for eukaryotic orthology analysis","volume":"38","author":"Ostlund","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20171013134712_gkt399-B12","doi-asserted-by":"crossref","first-page":"611","DOI":"10.1104\/pp.104.054452","article-title":"Phylogenomic analysis of the receptor-like proteins of rice and Arabidopsis","volume":"138","author":"Fritz-Laylin","year":"2005","journal-title":"Plant Physiol."},{"key":"key\n\t\t\t\t20171013134712_gkt399-B13","doi-asserted-by":"crossref","first-page":"D109","DOI":"10.1093\/nar\/gkr988","article-title":"KEGG for integration and interpretation of large-scale molecular data sets","volume":"40","author":"Kanehisa","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20171013134712_gkt399-B14","doi-asserted-by":"crossref","first-page":"D556","DOI":"10.1093\/nar\/gkq1109","article-title":"PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions","volume":"39","author":"Huerta-Cepas","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20171013134712_gkt399-B15","doi-asserted-by":"crossref","first-page":"D284","DOI":"10.1093\/nar\/gkr1060","article-title":"eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges","volume":"40","author":"Powell","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20171013134712_gkt399-B16","doi-asserted-by":"crossref","first-page":"D358","DOI":"10.1093\/nar\/gks1116","article-title":"OrthoDB: a hierarchical catalog of animal, fungal and bacterial orthologs","volume":"41","author":"Waterhouse","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20171013134712_gkt399-B17","first-page":"165","article-title":"Phylogenetic inference in protein superfamilies: analysis of SH2 domains","volume":"6","author":"Sj\u00f6lander","year":"1998","journal-title":"Proc. Int. Conf. Intell. Syst. Mol. Biol."},{"key":"key\n\t\t\t\t20171013134712_gkt399-B18","doi-asserted-by":"crossref","first-page":"e383","DOI":"10.1371\/journal.pone.0000383","article-title":"Assessing performance of orthology detection strategies applied to eukaryotic genomes","volume":"2","author":"Chen","year":"2007","journal-title":"PLoS One"},{"key":"key\n\t\t\t\t20171013134712_gkt399-B19","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1186\/gb-2009-10-9-403","article-title":"Joining forces in the quest for orthologs","volume":"10","author":"Gabaldon","year":"2009","journal-title":"Genome Biol."}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/nar\/article-pdf\/41\/W1\/W242\/16942581\/gkt399.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2018,4,2]],"date-time":"2018-04-02T10:41:17Z","timestamp":1522665677000},"score":1,"resource":{"primary":{"URL":"http:\/\/academic.oup.com\/nar\/article\/41\/W1\/W242\/1100976\/The-PhyloFacts-FATCAT-web-server-ortholog"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,5,18]]},"references-count":19,"journal-issue":{"issue":"W1","published-online":{"date-parts":[[2013,5,18]]},"published-print":{"date-parts":[[2013,7,1]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gkt399","relation":{},"ISSN":["1362-4962","0305-1048"],"issn-type":[{"value":"1362-4962","type":"electronic"},{"value":"0305-1048","type":"print"}],"subject":[],"published-other":{"date-parts":[[2013,7,1]]},"published":{"date-parts":[[2013,5,18]]}}}