Algorithm of OMA for large-scale orthology inference

• Published in: BMC bioinformatics Vol. 9; no. 1; p. 518
• Main Authors: Roth, Alexander CJ, Gonnet, Gaston H, Dessimoz, Christophe
• Format: Journal Article
• Language: English
• Published: London BioMed Central 04.12.2008; BioMed Central Ltd; BMC
• Subjects: Algorithms; Bioinformatics; Biomedical and Life Sciences; Computational biology; Computational Biology - methods; Computational Biology/Bioinformatics; Computer Appl. in Life Sciences; Evolution, Molecular; Genetic algorithms; Genetic research; Genomics; Life Sciences; Methodology; Methodology Article; Methods; Microarrays; Sequence Alignment; Switzerland; Duplication Event; Break Pair; Orthologous Group; Lateral Gene Transfer; Stable Pair
• ISSN: 1471-2105; 1471-2105
• DOI: 10.1186/1471-2105-9-518

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.