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Algorithm of OMA for large-scale orthology inference
Open accessAbstract
BACKGROUND: OMA 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. RESULTS: The 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. CONCLUSION: OMA contains several novel improvement ideas for orthology inference and provides a unique dataset of large-scale orthology assignments.
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OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes
Li, L., Stoeckert, C. J., & Roos, D. S. (2003) · Genome Research · doi:10.1101/gr.1224503 · Cited by 5,707
A minimal gene set for cellular life derived by comparison of complete bacterial genomes
Mushegian, A. R., & Koonin, E. V. (1996) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.93.19.10268 · Cited by 916
Database resources of the National Center for Biotechnology Information
Wheeler, D. L., Barrett, T., Benson, D. A., Bryant, S. H., Canese, K., Chetvernin, V., Church, D. M., DiCuccio, M., Edgar, R., Federhen, S., et al. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkl1031 · Cited by 734
eggNOG: automated construction and annotation of orthologous groups of genes
Jensen, L. J., Julien, P., Kuhn, M., von Mering, C., Muller, J., Doerks, T., & Bork, P. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm796 · Cited by 547
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Leevy, J. L., Khoshgoftaar, T. M., Bauder, R. A., & Seliya, N. (2018) · Journal of Big Data · doi:10.1186/s40537-018-0151-6 · Cited by 759
HaMStR: Profile hidden markov model based search for orthologs in ESTs
Ebersberger, I., Strauss, S., & von Haeseler, A. (2009) · BMC Evolutionary Biology · doi:10.1186/1471-2148-9-157 · Cited by 288
A rooted phylogeny resolves early bacterial evolution
Coleman, G. A., Davín, A. A., Mahendrarajah, T. A., Szánthó, L. L., Spang, A., Hugenholtz, P., Szöllősi, G. J., & Williams, T. A. (2021) · Science · doi:10.1126/science.abe0511 · Cited by 285
Spiralian Phylogeny Informs the Evolution of Microscopic Lineages
Laumer, C. E., Bekkouche, N., Kerbl, A., Goetz, F., Neves, R. C., Sørensen, M. V., Kristensen, R. M., Hejnol, A., Dunn, C. W., Giribet, G., et al. (2015) · Current Biology · doi:10.1016/j.cub.2015.06.068 · Cited by 278
Phylogenomics provides robust support for a two-domains tree of life
Williams, T. A., Cox, C. J., Foster, P. G., Szöllősi, G. J., & Embley, T. M. (2019) · Nature Ecology & Evolution · doi:10.1038/s41559-019-1040-x · Cited by 274
Metadata
- Authors
- Roth, A. C., Gonnet, G. H., & Dessimoz, C.
- Venue
- BMC Bioinformatics
- Published
- 2008-12
- Volume
- 9
- Issue
- 1
- Pages
- 518-518
- ISSN
- 1471-2105 (ISSN-L)
- OpenAlex
- W2044892321
- Cited by
- 179
- References
- 4
- FWCI
- 3.85
- Type
- journal article
- Language
- en
- Open access
- gold
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