OMA

Web based database interface for orthology prediction


OMA in a nutshell

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.

OMA’s inference algorithm consists of three main phases. First, to infer homologous sequences (sequences of common ancestry), all-against-all Smith-Waterman alignments are computed and significant matches are retained. Second, to infer orthologous pairs (the subset of homologs related by speciation events), mutually closest homologs are identified based on evolutionary distances, taking into account distance inference uncertainty and the possibility for differential gene losses (for more details, see Roth et al 2008). Third, these orthologs are clustered in two different ways, which are useful for different purposes: (a) we identify cliques of orthologous pairs (“OMA groups”), which are useful as marker genes for phylogenetic reconstruction and tend to be very specific; (b) we identify hierarchical orthologous groups (“HOGs”), groups of genes defined for particular taxonomic ranges and identify all genes that have descended from a common ancestral gene in that taxonomic range. Fore more details on the algorithm to infer HOGs from orthologous pairs, see Altenhoff et al. 2013.

The OMA pipeline can also run on custom genomic/transcriptomic data using the OMA stand-alone software, and it is even possible to combine precomputed data with custom data by exporting parts of the OMA database.

For more info on the feature of the OMA Browser, please consult the help pages accessible from the navigation bar in the top-right corner.


History

The OMA project was initiated in 2004 at ETH Zurich by Prof. Gaston Gonnet, with the goal of identifying orthologs among all publicly available genomes. At the time, most sequenced genomes were bacteria and only only few were eukaryotes. Several PhD students in his group became increasingly involved, in particular Adrian Schneider, Christophe Dessimoz, and Alexander Roth. Over the subsequent 10 years, OMA underwent 16 major releases, steadily increasing the number of genomes under consideration.


Graph showing growth of OMA over time.

The OMA Browser was introduced in 2006. Early releases were developed by Adrian Schneider and Christophe Dessimoz. Adrian Altenhoff joined the team in 2008.

In 2008, the responsibility of “baby-sitting” the all-against-all (i.e. importing and converting genomes, running and verifying computations across hundreds of CPUs) was handed over from Gaston to the two Adrians.

Since 2010, Adrian Altenhoff has been the main baby-sitter of the all-against-all and manager of OMA’s operations. In 2011, Christophe joined Gaston as co-PI of OMA. In 2012, OMA became a SIB-funded bioinformatics resource.


Publication

OMA overview


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 and Christophe Dessimoz
The OMA orthology database in 2015: function predictions, better plant support, synteny view, and other improvements
Nucleic Acids Research, 2015, 43 (D1): D240-D249 Full text


Adrian M. Altenhoff, Adrian Schneider, Gaston H. Gonnet, Christophe Dessimoz
OMA 2011: Orthology Inference Among 1,000 Complete Genomes
Nucleic Acids Research, 2011, 39 (suppl 1): D289-D294 Full text


Adrian Schneider, Christophe Dessimoz, Gaston H. Gonnet
OMA Browser - Exploring orthologous relations across 352 complete genomes
Bioinformatics, 2007, 23:16 (pp. 2180-2182) Project page Full text


OMA algorithm



Adrian M. Altenhoff, Manuel Gil, Gaston H. Gonnet, Christophe Dessimoz
Inferring Hierarchical Orthologous Groups From Orthologous Gene Pairs
PLoS One, 2013, 8:1, e53786 Software Full text


Alexander Roth, Gaston H. Gonnet, Christophe Dessimoz
Algorithm of OMA for Large-Scale Orthology Inference
BMC Bioinformatics, 2008, 9:518 Full text (Please note the associated erratum)


Christophe Dessimoz, Brigitte Boeckmann, Alexander Roth, Gaston H. Gonnet
Detecting Non-Orthology in the COGs Database and Other Approaches Grouping Orthologs Using Genome-Specific Best Hits
Nucleic Acids Res, 2006 34:11 (pp. 3309-3316) Full text


Christophe Dessimoz, Gina Cannarozzi, Manuel Gil, Daniel Margadant, Alexander Roth, Adrian Schneider, Gaston H. Gonnet
OMA, a Comprehensive, Automated Project for the Identification of Orthologs from Complete Genome Data: Introduction and First Achievements
RECOMB 2005 Workshop on Comparative Genomics, LNCS 3678 (pp. 61-72) Full text Abstract


Benchmarking



Daniel A. Dalquen, Adrian M. Altenhoff, Gaston H. Gonnet, Christophe Dessimoz
The Impact of Gene Duplication, Insertion, Deletion, Lateral Gene Transfer and Sequencing Error on Orthology Inference: a Simulation Study
PLoS One, 2013, 8:2, e56925 Full text


Brigitte Boeckmann, Marc Robinson-Rechavi, Ioannis Xenarios, Christophe Dessimoz
Conceptual Framework and Pilot Study to Benchmark Phylogenomic Databases Based on Reference Gene Trees
Briefings in Bioinformatics, 2011, 12:5 (pp. 474-484) Full text


Adrian M. Altenhoff and Christophe Dessimoz
Phylogenetic and Functional Assessment of Orthologs Inference Projects and Methods
PLoS Computational Biology, 2009, 5:1, e1000262 Full text


Orthology inference in general



Adrian M. Altenhoff and Christophe Dessimoz
Inferring Orthology and Paralogy Evolutionary Genomics: Statistical and Computational methods
(M Anisimova, Editor), Methods in Molecular Biology, 2012, Springer Humana, Vol. 855. Full text Abstract