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      OrthoDB: the hierarchical catalog of eukaryotic orthologs

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          Abstract

          The concept of orthology is widely used to relate genes across different species using comparative genomics, and it provides the basis for inferring gene function. Here we present the web accessible OrthoDB database that catalogs groups of orthologous genes in a hierarchical manner, at each radiation of the species phylogeny, from more general groups to more fine-grained delineations between closely related species. We used a COG-like and Inparanoid-like ortholog delineation procedure on the basis of all-against-all Smith-Waterman sequence comparisons to analyze 58 eukaryotic genomes, focusing on vertebrates, insects and fungi to facilitate further comparative studies. The database is freely available at http://cegg.unige.ch/orthodb

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          Most cited references21

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          Amino acid substitution matrices from protein blocks.

          Methods for alignment of protein sequences typically measure similarity by using a substitution matrix with scores for all possible exchanges of one amino acid with another. The most widely used matrices are based on the Dayhoff model of evolutionary rates. Using a different approach, we have derived substitution matrices from about 2000 blocks of aligned sequence segments characterizing more than 500 groups of related proteins. This led to marked improvements in alignments and in searches using queries from each of the groups.
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            Orthologs, paralogs, and evolutionary genomics.

            Orthologs and paralogs are two fundamentally different types of homologous genes that evolved, respectively, by vertical descent from a single ancestral gene and by duplication. Orthology and paralogy are key concepts of evolutionary genomics. A clear distinction between orthologs and paralogs is critical for the construction of a robust evolutionary classification of genes and reliable functional annotation of newly sequenced genomes. Genome comparisons show that orthologous relationships with genes from taxonomically distant species can be established for the majority of the genes from each sequenced genome. This review examines in depth the definitions and subtypes of orthologs and paralogs, outlines the principal methodological approaches employed for identification of orthology and paralogy, and considers evolutionary and functional implications of these concepts.
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              Distinguishing homologous from analogous proteins.

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                Author and article information

                Journal
                Nucleic Acids Res
                Nucleic Acids Res
                nar
                nar
                Nucleic Acids Research
                Oxford University Press
                0305-1048
                1362-4962
                January 2008
                18 October 2007
                18 October 2007
                : 36
                : Database issue , Database issue
                : D271-D275
                Affiliations
                1Department of Genetic Medicine and Development, University of Geneva Medical School, 2Swiss Institute of Bioinformatics, 1 rue Michel-Servet, 3Department of Structural Biology and Bioinformatics, University of Geneva Medical School, 1 rue Michel-Servet, 1211 Geneva, Switzerland and 4Imperial College London, South Kensington Campus, SW7 2AZ London, UK
                Author notes
                *To whom correspondence should be addressed.+41 22 379 59 73+41 22 379 57 06 evgeny.zdobnov@ 123456medecine.unige.ch
                Article
                10.1093/nar/gkm845
                2238902
                17947323
                9e67926a-74b9-4aa7-813c-61ed4585eced
                © 2007 The Author(s)

                This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 20 August 2007
                : 24 September 2007
                : 25 September 2007
                Categories
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                Genetics
                Genetics

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