The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements.
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.
University College London, Gower Street, London WC1E 6BT, UK Swiss Institute of Bioinformatics, Universitätstr. 6, 8092 Zurich, Switzerland ETH Zurich, Computer Science, Universitätstr. 6, 8092 Zurich, Switzerland.
Adrian M
AM
Altenhoff
University College London, Gower Street, London WC1E 6BT, UK Swiss Institute of Bioinformatics, Universitätstr. 6, 8092 Zurich, Switzerland ETH Zurich, Computer Science, Universitätstr. 6, 8092 Zurich, Switzerland.
Nives
N
Škunca
University College London, Gower Street, London WC1E 6BT, UK Institut National de la Recherche Agronomique (INRA) UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France Bayer CropScience NV, Technologiepark 38, 9052 Gent, Belgium.
Natasha
N
Glover
ETH Zurich, Computer Science, Universitätstr. 6, 8092 Zurich, Switzerland.
Clément-Marie
CM
Train
University College London, Gower Street, London WC1E 6BT, UK.
Anna
A
Sueki
University College London, Gower Street, London WC1E 6BT, UK.
Ivana
I
Piližota
European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Kevin
K
Gori
University College London, Gower Street, London WC1E 6BT, UK.
Bartlomiej
B
Tomiczek
University College London, Gower Street, London WC1E 6BT, UK.
Steven
S
Müller
Bayer CropScience NV, Technologiepark 38, 9052 Gent, Belgium.
Henning
H
Redestig
Swiss Institute of Bioinformatics, Universitätstr. 6, 8092 Zurich, Switzerland ETH Zurich, Computer Science, Universitätstr. 6, 8092 Zurich, Switzerland.
Gaston H
GH
Gonnet
University College London, Gower Street, London WC1E 6BT, UK European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK c.dessimoz@ucl.ac.uk.
Christophe
C
Dessimoz
D000465:Algorithms; D030562:Databases, Protein; D063990:Gene Ontology; D018745:Genome, Plant; D006801:Humans; D020407:Internet; D010940:Plant Proteins / Q000737:chemistry / Q000235:genetics*; D020543:Proteome / Q000737:chemistry* / Q000235:genetics; D017386:Sequence Homology, Amino Acid; D026801:Synteny; D014908:Triticum / Q000235:genetics
D010940:Plant Proteins; D020543:Proteome