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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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Gene losses, duplications and gains from hierarchical orthologous groups. Gene duplications, losses and gains on the primate lineage inferred from OMA hierarchical orthologous groups.
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Figure 6: Gene losses, duplications and gains from hierarchical orthologous groups. Gene duplications, losses and gains on the primate lineage inferred from OMA hierarchical orthologous groups.

Mentions: To illustrate this application, we provide an estimate of gains and losses in the primate tree obtained by parsing OMA HOGs (Figure 6). Large numbers of losses on terminal branches can be indicative of fragmentary genomes (45), such as the tarsier with its low 1.82x coverage. Even so, previous studies have reported elevated duplication and loss rates in the primate lineage (46).


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)

Gene losses, duplications and gains from hierarchical orthologous groups. Gene duplications, losses and gains on the primate lineage inferred from OMA hierarchical orthologous groups.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 6: Gene losses, duplications and gains from hierarchical orthologous groups. Gene duplications, losses and gains on the primate lineage inferred from OMA hierarchical orthologous groups.
Mentions: To illustrate this application, we provide an estimate of gains and losses in the primate tree obtained by parsing OMA HOGs (Figure 6). Large numbers of losses on terminal branches can be indicative of fragmentary genomes (45), such as the tarsier with its low 1.82x coverage. Even so, previous studies have reported elevated duplication and loss rates in the primate lineage (46).

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