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Database Commons - OMA

OMA

Citations: 153

z-index 13.99

Short name OMA
Full name The Orthologous Matrix project
Description The Orthologous Matrix (OMA) project is a method and associated database inferring evolutionary relationships amongst currently 1706 complete proteomes
URL http://omabrowser.org/oma/home/
Year founded 2011
Last update & version 2015-04-03    v1.0.2
Availability Free to all users
University/Institution hosted University College London
Address Gower Street,London WC1E 6BT,UK
City London
Province/State
Country/Region United Kingdom
Contact name Christophe Dessimoz
Contact email c.dessimoz@ucl.ac.uk
Data type(s)
Major organism(s)
Keyword(s)
  • orthologous matrix
Publication(s)
  • The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements. [PMID: 25399418]

    Adrian M Altenhoff, Nives Škunca, Natasha Glover, Clément-Marie Train, Anna Sueki, Ivana Piližota, Kevin Gori, Bartlomiej Tomiczek, Steven Müller, Henning Redestig, Gaston H Gonnet, Christophe Dessimoz
    Nucleic acids research 2015:43(Database issue)
    8 Citations (Google Scholar as of 2015-12-29)

    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. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  • OMA 2011: orthology inference among 1000 complete genomes. [PMID: 21113020]

    Adrian M Altenhoff, Adrian Schneider, Gaston H Gonnet, Christophe Dessimoz
    Nucleic acids research 2011:39(Database issue)
    145 Citations (Google Scholar as of 2016-05-02)

    Abstract: OMA (Orthologous MAtrix) is a database that identifies orthologs among publicly available, complete genomes. Initiated in 2004, the project is at its 11th release. It now includes 1000 genomes, making it one of the largest resources of its kind. Here, we describe recent developments in terms of species covered; the algorithmic pipeline--in particular regarding the treatment of alternative splicing, and new features of the web (OMA Browser) and programming interface (SOAP API). In the second part, we review the various representations provided by OMA and their typical applications. The database is publicly accessible at http://omabrowser.org.

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200 OK2017-02-17
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200 OK2016-12-20
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200 OK2016-12-13
200 OK2016-12-09
200 OK2016-12-06
200 OK2016-12-02
200 OK2016-11-29
200 OK2016-11-25
200 OK2016-11-22
200 OK2016-11-18
200 OK2016-11-15
200 OK2016-11-11
200 OK2016-11-08
200 OK2016-11-04
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200 OK2016-10-28
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200 OK2016-10-18
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200 OK2016-07-19
200 OK2016-07-15
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200 OK2016-07-08
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200 OK2016-05-03
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200 OK2016-04-19
200 OK2016-04-15
200 OK2016-04-12
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200 OK2016-02-01
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200 OK2016-01-29
200 OK2016-01-27
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200 OK2016-01-24
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200 OK2016-01-06
-1 Failed2016-01-04

Tags

DNA Protein
Archaea Bacteria Eukaryota
orthologous matrix

Record metadata

  • Created on: 2015-06-20
  • Curated by:
    • Lin Liu [2016-03-28]
    • Lina Ma [2015-11-17]
    • Li Yang [2015-06-26]
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