OMA
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).
License
Mozilla Public License (MPL) Version 2.0
Usage
Upcoming modulesystem change alert!
Due to large number of applications and their versions it is not practical to keep them explicitly listed at our wiki pages. Therefore an upgrade of modulefiles is underway. A feature of this upgrade will be the existence of default module for every application. This default choice does not need version number and it will load some (usually latest) version.
You can test the new version now by adding a line
source /cvmfs/software.metacentrum.cz/modulefiles/5.1.0/loadmodules
to your script before loading a module. Then, you can list all versions of oma and load default version of oma as
module avail oma/ # list available modules module load oma # load (default) module
If you wish to keep up to the current system, it is still possible. Simply list all modules by
module avail oma
and choose explicit version you want to use.
Documentation
Basic documentation is at http://omabrowser.org/standalone/ and https://www.biostars.org/t/oma/