OMA
OMA infers evolutionary relationships among 1706 complete proteomes by identifying orthologs through analysis of protein sequences associated with every protein-coding gene.
Key Features:
- Gene Ontology Function Predictions: Integrated predictions provide functional annotations of genes across species.
- Enhanced Support for Plant Genomes: Improved handling of homeologs and polyploidy, with specific attention to complex genomes such as wheat, to refine orthology inference.
- Synteny Viewer: Provides representation of the genomic context surrounding orthologous genes to assess gene conservation and rearrangements across species.
- Hierarchical Orthologous Groups (HOGs): Statically computed subsets of HOGs are available for download in OrthoXML format for detailed evolutionary analysis.
- Custom Data Integration: Export of parts of the all-against-all computations enables combination with custom datasets for client-side orthology prediction.
Scientific Applications:
- Comparative genomics: Identification of orthologs across 1706 proteomes to support cross-species comparisons and gene conservation studies.
- Evolutionary inference: Reconstruction of evolutionary relationships among genes and species using orthology assignments and HOGs.
- Functional annotation transfer: Propagation of Gene Ontology annotations across orthologs to infer gene function in less-characterized species.
- Plant genome analysis: Resolution of homeologs and polyploidy-related relationships in complex plant genomes such as wheat.
- Synteny and genome rearrangement analysis: Use of genomic context information to study conservation and rearrangements around orthologous genes.
- Custom orthology prediction: Integration of exported all-against-all results with user datasets for tailored orthology analyses.
Methodology:
Analysis of protein sequences associated with every protein-coding gene across genomes, execution of all-against-all computations, integration of Gene Ontology function predictions within the pipeline, and static computation of Hierarchical Orthologous Groups available in OrthoXML.
Topics
Details
- Tool Type:
- desktop application, web application
- Operating Systems:
- Linux, Windows, Mac
- Added:
- 6/24/2016
- Last Updated:
- 6/3/2025
Operations
Publications
Altenhoff AM, Škunca N, Glover N, Train C, Sueki A, Piližota I, Gori K, Tomiczek B, Müller S, Redestig H, Gonnet GH, Dessimoz C. The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements. Nucleic Acids Research. 2014;43(D1):D240-D249. doi:10.1093/nar/gku1158. PMID:25399418. PMCID:PMC4383958.
Altenhoff AM, Warwick Vesztrocy A, Bernard C, Train C, Nicheperovich A, Prieto Baños S, Julca I, Moi D, Nevers Y, Majidian S, Dessimoz C, Glover NM. OMA orthology in 2024: improved prokaryote coverage, ancestral and extant GO enrichment, a revamped synteny viewer and more in the OMA Ecosystem. Nucleic Acids Research. 2023;52(D1):D513-D521. doi:10.1093/nar/gkad1020. PMID:37962356. PMCID:PMC10767875.
Altenhoff AM, Train C, Gilbert KJ, Mediratta I, Mendes de Farias T, Moi D, Nevers Y, Radoykova H, Rossier V, Warwick Vesztrocy A, Glover NM, Dessimoz C. OMA orthology in 2021: website overhaul, conserved isoforms, ancestral gene order and more. Nucleic Acids Research. 2020;49(D1):D373-D379. doi:10.1093/nar/gkaa1007. PMID:33174605. PMCID:PMC7779010.
Altenhoff AM, Glover NM, Train C, Kaleb K, Warwick Vesztrocy A, Dylus D, de Farias TM, Zile K, Stevenson C, Long J, Redestig H, Gonnet GH, Dessimoz C. The OMA orthology database in 2018: retrieving evolutionary relationships among all domains of life through richer web and programmatic interfaces. Nucleic Acids Research. 2017;46(D1):D477-D485. doi:10.1093/nar/gkx1019. PMID:29106550. PMCID:PMC5753216.