OMA standalone: orthology inference among public and custom genomes and transcriptomes.

Details

Serval ID
serval:BIB_D405BD0232C3
Type
Article: article from journal or magazin.
Collection
Publications
Title
OMA standalone: orthology inference among public and custom genomes and transcriptomes.
Journal
Genome research
Author(s)
Altenhoff A.M., Levy J., Zarowiecki M., Tomiczek B., Warwick Vesztrocy A., Dalquen D.A., Müller S., Telford M.J., Glover N.M., Dylus D., Dessimoz C.
ISSN
1549-5469 (Electronic)
ISSN-L
1088-9051
Publication state
Published
Issued date
07/2019
Peer-reviewed
Oui
Volume
29
Number
7
Pages
1152-1163
Language
english
Notes
Publication types: Journal Article
Publication Status: ppublish
Abstract
Genomes and transcriptomes are now typically sequenced by individual laboratories but analyzing them often remains challenging. One essential step in many analyses lies in identifying orthologs-corresponding genes across multiple species-but this is far from trivial. The Orthologous MAtrix (OMA) database is a leading resource for identifying orthologs among publicly available, complete genomes. Here, we describe the OMA pipeline available as a standalone program for Linux and Mac. When run on a cluster, it has native support for the LSF, SGE, PBS Pro, and Slurm job schedulers and can scale up to thousands of parallel processes. Another key feature of OMA standalone is that users can combine their own data with existing public data by exporting genomes and precomputed alignments from the OMA database, which currently contains over 2100 complete genomes. We compare OMA standalone to other methods in the context of phylogenetic tree inference, by inferring a phylogeny of Lophotrochozoa, a challenging clade within the protostomes. We also discuss other potential applications of OMA standalone, including identifying gene families having undergone duplications/losses in specific clades, and identifying potential drug targets in nonmodel organisms. OMA standalone is available under the permissive open source Mozilla Public License Version 2.0.
Pubmed
Web of science
Open Access
Yes
Create date
08/07/2019 16:19
Last modification date
21/08/2019 5:33
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