Comparing Methods for Identifying Orthologs in Genomics
Author Information
Author(s): Adrian M. Altenhoff, Christophe Dessimoz
Primary Institution: Institute of Computational Science, ETH Zurich, and Swiss Institute of Bioinformatics, Zürich, Switzerland
Hypothesis
How do different ortholog identification methods compare in terms of accuracy and functionality?
Conclusion
The study found that OMA and Homologene performed best in both phylogenetic and functional tests, while simpler methods like Bidirectional Best Hit also showed good accuracy.
Supporting Evidence
- The study systematically compared nine leading orthology projects and two standard methods.
- OMA and Homologene were found to perform best in phylogenetic tests.
- OrthoMCL outperformed Ensembl Compara at lower functional specificity.
- EggNOG provided the largest coverage for coarse-grained functional categories.
Takeaway
This study looked at different ways to find similar genes in different species and found that some methods work better than others.
Methodology
The study compared predictions from 11 ortholog inference projects using phylogenetic and functional tests.
Limitations
The study's comparisons were limited by the availability of data and the varying sizes and methodologies of the different projects.
Digital Object Identifier (DOI)
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