ArticleBMC bioinformatics2008
Algorithm of OMA for large-scale orthology inference.
Article in BMC bioinformatics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 97 papers, 1 of them a synthesis that pooled it.
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Who cites it
97 citing papers in PubMed, 1 synthesis or guideline pooled it.
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- Large-scale experimental assessment of variant effects on the structure and function of the citrate transporter SLC13A5.Science advances · 2025Article
- New developments for the Quest for Orthologs benchmark service.NAR genomics and bioinformatics · 2024Article
- A conserved transcriptional program for MAIT cells across mammalian evolution.The Journal of experimental medicine · 2024Article
- Topological structures and syntenic conservation in sea anemone genomes.Nature communications · 2023Article
- Efficient gene orthology inference via large-scale rearrangements.Algorithms for molecular biology : AMB · 2023Article
- Elucidating the Mesocarp Drupe Transcriptome of Açai (International journal of molecular sciences · 2023Article
- HGD: an integrated homologous gene database across multiple species.Nucleic acids research · 2023Article
- Multilayered Networks of SalmoNet2 Enable Strain Comparisons of the Salmonella Genus on a Molecular Level.mSystems · 2022Article
- Positive Selection and Enhancer Evolution Shaped Lifespan and Body Mass in Great Apes.Molecular biology and evolution · 2022Article
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- Homoeolog Inference Methods Requiring Bidirectional Best Hits or Synteny Miss Many Pairs.Genome biology and evolution · 2021Article
- Complete Characterization of Incorrect Orthology Assignments in Best Match Graphs.Journal of mathematical biology · 2021Article
- CoreCruncher: Fast and Robust Construction of Core Genomes in Large Prokaryotic Data Sets.Molecular biology and evolution · 2021Article
- The origin and diversification of pteropods precede past perturbations in the Earth's carbon cycle.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Shedding light: a phylotranscriptomic perspective illuminates the origin of photosymbiosis in marine bivalves.BMC evolutionary biology · 2020Article
37 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundOMA is a project that aims to identify orthologs within publicly available, complete genomes. With 657 genomes analyzed to date, OMA is one of the largest projects of its kind.
resultsThe algorithm of OMA improves upon standard bidirectional best-hit approach in several respects: it uses evolutionary distances instead of scores, considers distance inference uncertainty, includes many-to-many orthologous relations, and accounts for differential gene losses. Herein, we describe in detail the algorithm for inference of orthology and provide the rationale for parameter selection through multiple tests.
conclusionOMA contains several novel improvement ideas for orthology inference and provides a unique dataset of large-scale orthology assignments.
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