Rock, paper, scissors: harnessing complementarity in ortholog detection methods improves comparative genomic inference.
Bottom Line: OD methods comprise a wide variety of approaches, each with their own benefits and costs under a variety of evolutionary and practical scenarios.In head-to-head comparisons, we find that these algorithms significantly outperform one another for 38-45% of the genes analyzed.Further, this improvement in alignment quality yields more confidently aligned sites and higher levels of overall conservation, while simultaneously detecting of up to 180% more positively selected sites.
Affiliation: Department of Epidemiology and Biostatistics, University of California, San Francisco, University of California, San Francisco, San Francisco, California.Show MeSH
Related in: MedlinePlus
Mentions: MOSAIC provides a highly flexible, graph-based framework for integrating diverse OD methods. For a given reference sequence, proposal orthologs are conceptualized as nodes in a graph, connected with edges weighted according to the pairwise similarity between sequences (Figure 1). The task of OD integration is then to choose proposal orthologs from each species such that a chosen measure of intra-cluster similarity is optimized.
Affiliation: Department of Epidemiology and Biostatistics, University of California, San Francisco, University of California, San Francisco, San Francisco, California.