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The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements

Altenhoff, Adrian M. ; Škunca, Nives ; Glover, Natasha ; Train, Clément-Marie ; Sueki, Anna ; Piližota, Ivana ; Gori, Kevin ; Tomiczek, Bartlomiej ; Müller, Steven ; Redestig, Henning ; Gonnet, Gaston H. ; Dessimoz, Christophe

In: Nucleic Acids Research, 2015, vol. 43, no. D1, p. D240-D249

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    Titel
    • The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements
    Autor
    • Altenhoff, Adrian M.. University College London, Gower Street, London WC1E 6BT, UK
    • Škunca, Nives. University College London, Gower Street, London WC1E 6BT, UK
    • Glover, Natasha. University College London, Gower Street, London WC1E 6BT, UK
    • Train, Clément-Marie. ETH Zurich, Computer Science, Universitätstr. 6, 8092 Zurich, Switzerland
    • Sueki, Anna. University College London, Gower Street, London WC1E 6BT, UK
    • Piližota, Ivana. University College London, Gower Street, London WC1E 6BT, UK
    • Gori, Kevin. European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    • Tomiczek, Bartlomiej. University College London, Gower Street, London WC1E 6BT, UK
    • Müller, Steven. University College London, Gower Street, London WC1E 6BT, UK
    • Redestig, Henning. Bayer CropScience NV, Technologiepark 38, 9052 Gent, Belgium
    • Gonnet, Gaston H.. Swiss Institute of Bioinformatics, Universitätstr. 6, 8092 Zurich, Switzerland
    • Dessimoz, Christophe. University College London, Gower Street, London WC1E 6BT, UK
    Dokumententyp
    • Postprint
    Sprache
    • Englisch
    Veröffentlicht in
    • Nucleic Acids Research, 2015, vol. 43, no. D1, p. D240-D249. Oxford University Press
    Andere elektronische Ausgabe
    Klassifikation
    • Gesundheit
    OAI-PMH-ID
    • oai:doc.rero.ch:296445
    Summary
    The Orthologous Matrix (OMA) project is a method and associated database inferring evolutionary relationships amongst currently 1706 complete proteomes (i.e. the protein sequence associated for every protein-coding gene in all genomes). In this update article, we present six major new developments in OMA: (i) a new web interface; (ii) Gene Ontology function predictions as part of the OMA pipeline; (iii) better support for plant genomes and in particular homeologs in the wheat genome; (iv) a new synteny viewer providing the genomic context of orthologs; (v) statically computed hierarchical orthologous groups subsets downloadable in OrthoXML format; and (vi) possibility to export parts of the all-against-all computations and to combine them with custom data for ‘client-side' orthology prediction. OMA can be accessed through the OMA Browser and various programmatic interfaces at http://omabrowser.org