Improving the specificity of high-throughput ortholog prediction

Background: Orthologs (genes that have diverged after a speciation event) tend to have similar function, and so their prediction has become an important component of comparative genomics and genome annotation. The gold standard phylogenetic analysis approach of comparing available organismal phylogeny to gene phylogeny is not easily automated for genome-wide analysis; therefore, ortholog prediction for large genome-scale datasets is typically performed using a reciprocal-best-BLAST-hits (RBH) approach. One problem with RBH is that it will incorrectly predict a paralog as an ortholog when incomplete genome sequences or gene loss is involved. In addition, there is an increasing interest in identifying orthologs most likely to have retained similar function. Results: To address these issues, we present here a high-throughput computational method named Ortholuge that further evaluates previously predicted orthologs (including those predicted using an RBH-based approach)

• Type: Journal
• Year: 2006
• Where: BMCBI
• Authors: Debra L. Fulton, Yvonne Y. Li, Matthew R. Laird, Benjamin G. S. Horsman, Fiona M. Roche, Fiona S. L. Brinkman
• Keywords: BMCBI 2006, Incomplete Genome, Orthologs, Similar Function