OMA

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Description

The OMA (“Orthologous MAtrix”) project is a method and database for the inference of orthologs among complete genomes. The distinctive features of OMA are its broad scope and size, high quality of inferences, feature-rich web interface, availability of data in a wide range of formats and interfaces, and frequent update schedule of two releases per year. The process works in 4 phases:

  • All-against-all, the pairwise alignments between every pair of proteins of all genomes (“all-against-all”). For significant ones, an evolutionary distance is estimated in PAM units.2.
  • Formation of “stable pairs” (SPs), the mutually closest pairs within a confidence interval, to avoid exclusion of n:m orthologs.
  • Detection of paralogs among SPs using witnesses of non-orthology [2]. Pairs surviving this step are named “verified pairs” (VPs). At this point, they are very likely to be orthologs.
  • Formation of OMA groups, made of a subset of proteins in which all pairs are VPs (clique).

Availability

Version 0.99y. Freely available to users. Modules:

oma-0.99y

Licence

Mozilla Public License (MPL) Version 2.0

Use

Initialize environment with command:

module add oma-0.99y

Documentation

Basic documentation is at http://omabrowser.org/standalone/ and https://www.biostars.org/t/oma/

Program manager

meta@cesnet.cz

Homepage

http://omabrowser.org