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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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User-centric new design. The website has been redesigned with an emphasis on usability.
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Figure 1: User-centric new design. The website has been redesigned with an emphasis on usability.

Mentions: The OMA browser has been reorganised and redesigned to make it user-friendlier. The menu bar provides a consistent and persistent overview of all main functionalities. The documentation and help pages have been restructured and extended. The new ‘responsive’ layout takes advantage of large contemporary screens whilst also accommodating small screens such as smartphones and tablets. The landing page now provides pointers to introductory explanations for new users and recent announcements for returning users (Figure 1).


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)

User-centric new design. The website has been redesigned with an emphasis on usability.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 1: User-centric new design. The website has been redesigned with an emphasis on usability.
Mentions: The OMA browser has been reorganised and redesigned to make it user-friendlier. The menu bar provides a consistent and persistent overview of all main functionalities. The documentation and help pages have been restructured and extended. The new ‘responsive’ layout takes advantage of large contemporary screens whilst also accommodating small screens such as smartphones and tablets. The landing page now provides pointers to introductory explanations for new users and recent announcements for returning users (Figure 1).

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