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      Large-scale assignment of orthology: back to phylogenetics?

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      Author(s): 1 ,
      Publication date (Electronic):
      Journal: Genome Biology
      Publisher: BioMed Central

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          Abstract

          Automated use of phylogenetic trees to deduce orthology relationships in proteins.

          Abstract

          Reliable orthology prediction is central to comparative genomics. Although orthology is defined by phylogenetic criteria, most automated prediction methods are based on pairwise sequence comparisons. Recently, automated phylogeny-based orthology prediction has emerged as a feasible alternative for genome-wide studies.

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          Orthologs, paralogs, and evolutionary genomics.

          Eugene V. Koonin (2005)
          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.
          Article 0 comments Cited 470 times – based on 0 reviews     Review now
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            Distinguishing homologous from analogous proteins.

            W. M. Fitch (1970)
            Article 0 comments Cited 438 times – based on 0 reviews     Review now
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              Inparanoid: a comprehensive database of eukaryotic orthologs

              Kevin P. O'Brien, Maido Remm, Erik L. L. Sonnhammer (2004)
              The Inparanoid eukaryotic ortholog database (http://inparanoid.cgb.ki.se/) is a collection of pairwise ortholog groups between 17 whole genomes; Anopheles gambiae, Caenorhabditis briggsae, Caenorhabditis elegans, Drosophila melanogaster, Danio rerio, Takifugu rubripes, Gallus gallus, Homo sapiens, Mus musculus, Pan troglodytes, Rattus norvegicus, Oryza sativa, Plasmodium falciparum, Arabidopsis thaliana, Escherichia coli, Saccharomyces cerevisiae and Schizosaccharomyces pombe. Complete proteomes for these genomes were derived from Ensembl and UniProt and compared pairwise using Blast, followed by a clustering step using the Inparanoid program. An Inparanoid cluster is seeded by a reciprocally best-matching ortholog pair, around which inparalogs (should they exist) are gathered independently, while outparalogs are excluded. The ortholog clusters can be searched on the website using Ensembl gene/protein or UniProt identifiers, annotation text or by Blast alignment against our protein datasets. The entire dataset can be downloaded, as can the Inparanoid program itself.
              Article 0 comments Cited 310 times – based on 0 reviews     Review now
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                Author and article information

                Journal
                Journal ID (nlm-ta): Genome Biol
                Title: Genome Biology
                Publisher: BioMed Central
                ISSN (Print): 1465-6906
                ISSN (Electronic): 1465-6914
                Publication date (Print): 2008
                Publication date (Electronic): 30 October 2008
                Volume: 9
                Issue: 10
                Page: 235
                Affiliations
                [1 ]Bioinformatics and Genomics Program, Center for Genomic Regulation, Doctor Aiguader, 88, 08003 Barcelona, Spain
                Article
                Publisher ID: gb-2008-9-10-235
                DOI: 10.1186/gb-2008-9-10-235
                PMC ID: 2760865
                PubMed ID: 18983710
                SO-VID: ba9d2af1-b7e8-47cf-849a-47fac7fc4da7
                Copyright © Copyright © 2008 BioMed Central Ltd
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                Subject: Review

                ScienceOpen disciplines: Genetics
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                ScienceOpen disciplines: Genetics

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