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

Altenhoff AM, Škunca N, Glover N, Train CM, Sueki A, Piližota I, Gori K, Tomiczek B, Müller S, Redestig H, Gonnet GH, Dessimoz C - Nucleic Acids Res. (2014)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: 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.

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Numbers of electronic Gene Ontology annotations in the OMA database. Three major sources of electronic annotations are shown: annotations through the association of InterPro records with GO terms, annotations based on UniProtKB keyword mappings and annotations inferred in the OMA pipeline. The intersections show the numbers of annotations in common amongst the resources.
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Figure 3: Numbers of electronic Gene Ontology annotations in the OMA database. Three major sources of electronic annotations are shown: annotations through the association of InterPro records with GO terms, annotations based on UniProtKB keyword mappings and annotations inferred in the OMA pipeline. The intersections show the numbers of annotations in common amongst the resources.

Mentions: Overall, the OMA database now provides 442 376 477 function annotations for 7 947 728 proteins (Figure 3). Amongst the available annotations, most are computationally inferred; our own predictions constitute about 20% of the available annotations.


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

Altenhoff AM, Škunca N, Glover N, Train CM, Sueki A, Piližota I, Gori K, Tomiczek B, Müller S, Redestig H, Gonnet GH, Dessimoz C - Nucleic Acids Res. (2014)

Numbers of electronic Gene Ontology annotations in the OMA database. Three major sources of electronic annotations are shown: annotations through the association of InterPro records with GO terms, annotations based on UniProtKB keyword mappings and annotations inferred in the OMA pipeline. The intersections show the numbers of annotations in common amongst the resources.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4383958&req=5

Figure 3: Numbers of electronic Gene Ontology annotations in the OMA database. Three major sources of electronic annotations are shown: annotations through the association of InterPro records with GO terms, annotations based on UniProtKB keyword mappings and annotations inferred in the OMA pipeline. The intersections show the numbers of annotations in common amongst the resources.
Mentions: Overall, the OMA database now provides 442 376 477 function annotations for 7 947 728 proteins (Figure 3). Amongst the available annotations, most are computationally inferred; our own predictions constitute about 20% of the available annotations.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: 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.

Show MeSH