OrthoDB v8: update of the hierarchical catalog of orthologs and the underlying free software

Article Article scientifique Article OrthoDB v8: update of the hierarchical catalog of orthologs and the underlying free software eng 2015 author Kriventseva Evgenia 640181 author Tegenfeldt Fredrik 708726 author Petty Tom author Waterhouse Robert 654311 author Simao Neto Felipe 731423 author Pozdnyakov Igor 795352 author Ioannidis Panagiotis 808429 author Zdobnov Evgeny 636914 D250-256 10.1093/nar/gku1220 25428351 0305-1048 Orthology, refining the concept of homology, is the cornerstone of evolutionary comparative studies. With the ever-increasing availability of genomic data, inference of orthology has become instrumental for generating hypotheses about gene functions crucial to many studies. This update of the OrthoDB hierarchical catalog of orthologs (http://www.orthodb.org) covers 3027 complete genomes, including the most comprehensive set of 87 arthropods, 61 vertebrates, 227 fungi and 2627 bacteria (sampling the most complete and representative genomes from over 11,000 available). In addition to the most extensive integration of functional annotations from UniProt, InterPro, GO, OMIM, model organism phenotypes and COG functional categories, OrthoDB uniquely provides evolutionary annotations including rates of ortholog sequence divergence, copy-number profiles, sibling groups and gene architectures. We re-designed the entirety of the OrthoDB website from the underlying technology to the user interface, enabling the user to specify species of interest and to select the relevant orthology level by the NCBI taxonomy. The text searches allow use of complex logic with various identifiers of genes, proteins, domains, ontologies or annotation keywords and phrases. Gene copy-number profiles can also be queried. This release comes with the freely available underlying ortholog clustering pipeline (http://www.orthodb.org/software). Algorithms Animals Data Curation Databases, Genetic Eukaryota/genetics Evolution, Molecular Genome, Microbial Humans Sequence Homology Software Dewey 576.5 135 Département de médecine génétique et développement 21D false 493 Génomique Evolutionnaire Computationnelle 830 Nucleic acids research 43 Database issue c40e7370-6b36-4341-9804-d9b3bfd3c768 Article (Published version) Public Nucl. Acids Res.-2015-Kriventseva-D250-6.pdf 1261693 application/pdf openAccess Faculté de médecine / Section de médecine fondamentale / Département de médecine génétique et développement

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OrthoDB v8: update of the hierarchical catalog of orthologs and the underlying free software	Nucleic acids research			2015	717	601

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Pozdnyakov, Igor