{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,18]],"date-time":"2026-02-18T00:09:57Z","timestamp":1771373397379,"version":"3.50.1"},"reference-count":49,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2016,11,9]],"date-time":"2016-11-09T00:00:00Z","timestamp":1478649600000},"content-version":"vor","delay-in-days":725,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,1,28]]},"DOI":"10.1093\/nar\/gku1158","type":"journal-article","created":{"date-parts":[[2014,11,15]],"date-time":"2014-11-15T20:27:21Z","timestamp":1416083241000},"page":"D240-D249","source":"Crossref","is-referenced-by-count":196,"title":["The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements"],"prefix":"10.1093","volume":"43","author":[{"given":"Adrian M.","family":"Altenhoff","sequence":"first","affiliation":[]},{"given":"Nives","family":"\u0160kunca","sequence":"additional","affiliation":[]},{"given":"Natasha","family":"Glover","sequence":"additional","affiliation":[]},{"given":"Cl\u00e9ment-Marie","family":"Train","sequence":"additional","affiliation":[]},{"given":"Anna","family":"Sueki","sequence":"additional","affiliation":[]},{"given":"Ivana","family":"Pili\u017eota","sequence":"additional","affiliation":[]},{"given":"Kevin","family":"Gori","sequence":"additional","affiliation":[]},{"given":"Bartlomiej","family":"Tomiczek","sequence":"additional","affiliation":[]},{"given":"Steven","family":"M\u00fcller","sequence":"additional","affiliation":[]},{"given":"Henning","family":"Redestig","sequence":"additional","affiliation":[]},{"given":"Gaston H.","family":"Gonnet","sequence":"additional","affiliation":[]},{"given":"Christophe","family":"Dessimoz","sequence":"additional","affiliation":[]}],"member":"286","published-online":{"date-parts":[[2014,11,15]]},"reference":[{"key":"key\n\t\t\t\t20171011224447_B1","doi-asserted-by":"crossref","first-page":"99","DOI":"10.2307\/2412448","article-title":"Distinguishing homologous from analogous proteins","volume":"19","author":"Fitch","year":"1970","journal-title":"Syst. Zool."},{"key":"key\n\t\t\t\t20171011224447_B2","doi-asserted-by":"crossref","first-page":"619","DOI":"10.1016\/S0168-9525(02)02793-2","article-title":"Orthology, paralogy and proposed classification for paralog subtypes","volume":"18","author":"Sonnhammer","year":"2002","journal-title":"Trends Genet."},{"key":"key\n\t\t\t\t20171011224447_B3","doi-asserted-by":"crossref","first-page":"360","DOI":"10.1038\/nrg3456","article-title":"Functional and evolutionary implications of gene orthology","volume":"14","author":"Gabald\u00f3n","year":"2013","journal-title":"Nat. Rev. Genet."},{"key":"key\n\t\t\t\t20171011224447_B4","doi-asserted-by":"crossref","first-page":"2993","DOI":"10.1093\/bioinformatics\/btu492","article-title":"Big data and other challenges in the quest for orthologs","volume":"30","author":"Sonnhammer","year":"2014","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20171011224447_B5","doi-asserted-by":"crossref","first-page":"259","DOI":"10.1007\/978-1-61779-582-4_9","article-title":"Inferring orthology and paralogy","volume-title":"Evolutionary Genomics. Methods in Molecular Biology","author":"Altenhoff","year":"2012"},{"key":"key\n\t\t\t\t20171011224447_B6","doi-asserted-by":"crossref","first-page":"D231","DOI":"10.1093\/nar\/gkt1253","article-title":"eggNOG v4.0: nested orthology inference across 3686 organisms","volume":"42","author":"Powell","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20171011224447_B7","doi-asserted-by":"crossref","first-page":"D48","DOI":"10.1093\/nar\/gks1236","article-title":"Ensembl 2013","volume":"41","author":"Flicek","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20171011224447_B8","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":"\u00d6stlund","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20171011224447_B9","doi-asserted-by":"crossref","first-page":"D631","DOI":"10.1093\/nar\/gks1006","article-title":"MBGD update 2013: the microbial genome database for exploring the diversity of microbial world","volume":"41","author":"Uchiyama","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20171011224447_B10","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\t20171011224447_B11","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\t20171011224447_B12","doi-asserted-by":"crossref","first-page":"D377","DOI":"10.1093\/nar\/gks1118","article-title":"PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees","volume":"41","author":"Mi","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20171011224447_B13","doi-asserted-by":"crossref","first-page":"D897","DOI":"10.1093\/nar\/gkt1177","article-title":"PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome","volume":"42","author":"Huerta-Cepas","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20171011224447_B14","doi-asserted-by":"crossref","first-page":"3718","DOI":"10.1105\/tpc.109.071506","article-title":"PLAZA: a comparative genomics resource to study gene and genome evolution in plants","volume":"21","author":"Proost","year":"2009","journal-title":"Plant Cell"},{"key":"key\n\t\t\t\t20171011224447_B15","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\t20171011224447_B16","doi-asserted-by":"crossref","first-page":"e1000262","DOI":"10.1371\/journal.pcbi.1000262","article-title":"Phylogenetic and functional assessment of orthologs inference projects and methods","volume":"5","author":"Altenhoff","year":"2009","journal-title":"PLoS Comput. Biol."},{"key":"key\n\t\t\t\t20171011224447_B17","doi-asserted-by":"crossref","first-page":"W242","DOI":"10.1093\/nar\/gkt399","article-title":"The PhyloFacts FAT-CAT web server: ortholog identification and function prediction using fast approximate tree classification","volume":"41","author":"Afrasiabi","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20171011224447_B18","doi-asserted-by":"crossref","first-page":"423","DOI":"10.1093\/bib\/bbr034","article-title":"Conceptual framework and pilot study to benchmark phylogenomic databases based on reference gene trees","volume":"12","author":"Boeckmann","year":"2011","journal-title":"Brief. Bioinform."},{"key":"key\n\t\t\t\t20171011224447_B19","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1186\/1471-2105-12-11","article-title":"OrthoInspector: comprehensive orthology analysis and visual exploration","volume":"12","author":"Linard","year":"2011","journal-title":"BMC Bioinformatics"},{"key":"key\n\t\t\t\t20171011224447_B20","doi-asserted-by":"crossref","first-page":"518","DOI":"10.1186\/1471-2105-9-518","article-title":"Algorithm of OMA for large-scale orthology inference","volume":"9","author":"Roth","year":"2008","journal-title":"BMC Bioinformatics"},{"key":"key\n\t\t\t\t20171011224447_B21","doi-asserted-by":"crossref","first-page":"3309","DOI":"10.1093\/nar\/gkl433","article-title":"Detecting non-orthology in the COGs database and other approaches grouping orthologs using genome-specific best hits","volume":"34","author":"Dessimoz","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20171011224447_B22","doi-asserted-by":"crossref","first-page":"e53786","DOI":"10.1371\/journal.pone.0053786","article-title":"Inferring hierarchical orthologous groups from orthologous gene pairs","volume":"8","author":"Altenhoff","year":"2013","journal-title":"PLoS One"},{"key":"key\n\t\t\t\t20171011224447_B23","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1038\/75556","article-title":"Gene ontology: tool for the unification of biology. The Gene Ontology Consortium","volume":"25","author":"Ashburner","year":"2000","journal-title":"Nat. Genet."},{"key":"key\n\t\t\t\t20171011224447_B24","doi-asserted-by":"crossref","first-page":"D565","DOI":"10.1093\/nar\/gkr1048","article-title":"The UniProt-GO Annotation database in 2011","volume":"40","author":"Dimmer","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20171011224447_B25","doi-asserted-by":"crossref","first-page":"e1002852","DOI":"10.1371\/journal.pcbi.1002852","article-title":"Phyletic profiling with cliques of orthologs is enhanced by signatures of paralogy relationships","volume":"9","author":"Skunca","year":"2013","journal-title":"PLoS Comput. Biol."},{"key":"key\n\t\t\t\t20171011224447_B26","doi-asserted-by":"crossref","first-page":"D563","DOI":"10.1093\/nar\/gkp871","article-title":"Ensembl Genomes: extending Ensembl across the taxonomic space","volume":"38","author":"Kersey","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20171011224447_B27","doi-asserted-by":"crossref","first-page":"D1193","DOI":"10.1093\/nar\/gkt1110","article-title":"Gramene 2013: comparative plant genomics resources","volume":"42","author":"Monaco","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20171011224447_B28","doi-asserted-by":"crossref","first-page":"D1095","DOI":"10.1093\/nar\/gkq811","article-title":"GreenPhylDB v2.0: comparative and functional genomics in plants","volume":"39","author":"Rouard","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20171011224447_B29","doi-asserted-by":"crossref","first-page":"590","DOI":"10.1104\/pp.111.189514","article-title":"Dissecting plant genomes with the PLAZA comparative genomics platform","volume":"158","author":"Van Bel","year":"2012","journal-title":"Plant Physiol."},{"key":"key\n\t\t\t\t20171011224447_B30","doi-asserted-by":"crossref","first-page":"64","DOI":"10.1126\/science.1150646","article-title":"The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants","volume":"319","author":"Rensing","year":"2008","journal-title":"Science"},{"key":"key\n\t\t\t\t20171011224447_B31","doi-asserted-by":"crossref","first-page":"1250092","DOI":"10.1126\/science.1250092","article-title":"Ancient hybridizations among the ancestral genomes of bread wheat","volume":"345","author":"International Wheat Genome Sequencing Consortium","year":"2014","journal-title":"Science"},{"key":"key\n\t\t\t\t20171011224447_B32","doi-asserted-by":"crossref","first-page":"1251788","DOI":"10.1126\/science.1251788","article-title":"A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome","volume":"345","author":"International Wheat Genome Sequencing Consortium (IWGSC)","year":"2014","journal-title":"Science"},{"key":"key\n\t\t\t\t20171011224447_B33","doi-asserted-by":"crossref","first-page":"15780","DOI":"10.1073\/pnas.0908195106","article-title":"Genome comparisons reveal a dominant mechanism of chromosome number reduction in grasses and accelerated genome evolution in Triticeae","volume":"106","author":"Luo","year":"2009","journal-title":"Proc. Natl Acad. Sci. U.S.A."},{"key":"key\n\t\t\t\t20171011224447_B34","doi-asserted-by":"crossref","first-page":"252","DOI":"10.1104\/pp.112.205161","article-title":"Comparative analysis of syntenic genes in grass genomes reveals accelerated rates of gene structure and coding sequence evolution in polyploid wheat","volume":"161","author":"Akhunov","year":"2013","journal-title":"Plant Physiol."},{"key":"key\n\t\t\t\t20171011224447_B35","doi-asserted-by":"crossref","first-page":"1249721","DOI":"10.1126\/science.1249721","article-title":"Structural and functional partitioning of bread wheat chromosome 3B","volume":"345","author":"Choulet","year":"2014","journal-title":"Science"},{"key":"key\n\t\t\t\t20171011224447_B36","doi-asserted-by":"crossref","first-page":"212","DOI":"10.1186\/gb-2006-7-4-212","article-title":"Plant NBS-LRR proteins: adaptable guards","volume":"7","author":"McHale","year":"2006","journal-title":"Genome Biol."},{"key":"key\n\t\t\t\t20171011224447_B37","doi-asserted-by":"crossref","first-page":"1499","DOI":"10.1093\/oxfordjournals.molbev.a026249","article-title":"Rapid evolution of the family of CONSTANS LIKE genes in plants","volume":"17","author":"Lagercrantz","year":"2000","journal-title":"Mol. Biol. Evol."},{"key":"key\n\t\t\t\t20171011224447_B38","doi-asserted-by":"crossref","first-page":"130","DOI":"10.1186\/1471-2164-8-130","article-title":"Genes encoding pentatricopeptide repeat (PPR) proteins are not conserved in location in plant genomes and may be subject to diversifying selection","volume":"8","author":"Geddy","year":"2007","journal-title":"BMC Genomics"},{"key":"key\n\t\t\t\t20171011224447_B39","doi-asserted-by":"crossref","first-page":"1456","DOI":"10.1101\/gr.3672305","article-title":"The Yeast Gene Order Browser: combining curated homology and syntenic context reveals gene fate in polyploid species","volume":"15","author":"Byrne","year":"2005","journal-title":"Genome Res."},{"key":"key\n\t\t\t\t20171011224447_B40","doi-asserted-by":"crossref","first-page":"D700","DOI":"10.1093\/nar\/gks1156","article-title":"Genomicus: five genome browsers for comparative genomics in eukaryota","volume":"41","author":"Louis","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20171011224447_B41","doi-asserted-by":"crossref","first-page":"bat058","DOI":"10.1093\/database\/bat058","article-title":"GnpIS: an information system to integrate genetic and genomic data from plants and fungi","volume":"2013","author":"Steinbach","year":"2013","journal-title":"Database"},{"key":"key\n\t\t\t\t20171011224447_B42","doi-asserted-by":"crossref","first-page":"e41175","DOI":"10.1371\/journal.pone.0041175","article-title":"The natural history of class I primate alcohol dehydrogenases includes gene duplication, gene loss, and gene conversion","volume":"7","author":"Carrigan","year":"2012","journal-title":"PLoS One"},{"key":"key\n\t\t\t\t20171011224447_B43","doi-asserted-by":"crossref","first-page":"485","DOI":"10.1093\/bib\/bbr025","article-title":"Letter to the editor: SeqXML and OrthoXML: standards for sequence and orthology information","volume":"12","author":"Schmitt","year":"2011","journal-title":"Brief. Bioinform."},{"key":"key\n\t\t\t\t20171011224447_B44","doi-asserted-by":"crossref","first-page":"1269","DOI":"10.1093\/bioinformatics\/btl097","article-title":"CAFE: a computational tool for the study of gene family evolution","volume":"22","author":"De Bie","year":"2006","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20171011224447_B45","doi-asserted-by":"crossref","first-page":"R16","DOI":"10.1186\/gb-2010-11-2-r16","article-title":"2X genomes\u2013depth does matter","volume":"11","author":"Milinkovitch","year":"2010","journal-title":"Genome Biol."},{"key":"key\n\t\t\t\t20171011224447_B46","doi-asserted-by":"crossref","first-page":"552","DOI":"10.1038\/nrg1895","article-title":"Primate segmental duplications: crucibles of evolution, diversity and disease","volume":"7","author":"Bailey","year":"2006","journal-title":"Nat. Rev. Genet."},{"key":"key\n\t\t\t\t20171011224447_B47","doi-asserted-by":"crossref","first-page":"107","DOI":"10.1186\/1756-0500-1-107","article-title":"SWPS3 - fast multi-threaded vectorized Smith-Waterman for IBM Cell\/B.E. and x86\/SSE2","volume":"1","author":"Szalkowski","year":"2008","journal-title":"BMC Res. Notes"},{"key":"key\n\t\t\t\t20171011224447_B48","doi-asserted-by":"crossref","first-page":"e607","DOI":"10.7717\/peerj.607","article-title":"Speeding up all-against-all protein comparisons while maintaining sensitivity by considering subsequence-level homology","volume":"2","author":"Wittwer","year":"2014","journal-title":"PeerJ"},{"key":"key\n\t\t\t\t20171011224447_B49","doi-asserted-by":"crossref","first-page":"474","DOI":"10.1093\/bib\/bbr038","article-title":"Comparative genomics approach to detecting split-coding regions in a low-coverage genome: lessons from the chimaera Callorhinchus milii (Holocephali, Chondrichthyes)","volume":"12","author":"Dessimoz","year":"2011","journal-title":"Brief. Bioinform."}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/nar\/article-pdf\/43\/D1\/D240\/17437130\/gku1158.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2018,4,2]],"date-time":"2018-04-02T10:41:48Z","timestamp":1522665708000},"score":1,"resource":{"primary":{"URL":"http:\/\/academic.oup.com\/nar\/article\/43\/D1\/D240\/2438427\/The-OMA-orthology-database-in-2015-function"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,11,15]]},"references-count":49,"journal-issue":{"issue":"D1","published-online":{"date-parts":[[2014,11,15]]},"published-print":{"date-parts":[[2015,1,28]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gku1158","relation":{},"ISSN":["1362-4962","0305-1048"],"issn-type":[{"value":"1362-4962","type":"electronic"},{"value":"0305-1048","type":"print"}],"subject":[],"published-other":{"date-parts":[[2015,1,28]]},"published":{"date-parts":[[2014,11,15]]}}}