The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements.
Details
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UNIL restricted access
State: Public
Version: Final published version
License: Not specified
Serval ID
serval:BIB_0E374421DCD4
Type
Article: article from journal or magazin.
Collection
Publications
Institution
Title
The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements.
Journal
Nucleic acids research
ISSN
1362-4962 (Electronic)
ISSN-L
0305-1048
Publication state
Published
Issued date
01/2015
Peer-reviewed
Oui
Volume
43
Number
Database issue
Pages
D240-9
Language
english
Notes
Publication types: Journal Article ; Research Support, Non-U.S. Gov't
Publication Status: ppublish
Publication Status: ppublish
Abstract
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.
Keywords
Algorithms, Databases, Protein, Gene Ontology, Genome, Plant, Humans, Internet, Plant Proteins/chemistry, Plant Proteins/genetics, Proteome/chemistry, Proteome/genetics, Sequence Homology, Amino Acid, Synteny, Triticum/genetics
Pubmed
Web of science
Open Access
Yes
Create date
02/09/2015 8:16
Last modification date
09/08/2024 14:53