Orthology prediction at scalable resolution by phylogenetic tree analysis

Background: Orthology is one of the cornerstones of gene function prediction. Dividing the phylogenetic relations between genes into either orthologs or paralogs is however an oversimplification. Already in two-species gene-phylogenies, the complicated, non-transitive nature of phylogenetic relations results in inparalogs and outparalogs. For situations with more than two species we lack semantics to specifically describe the phylogenetic relations, let alone to exploit them. Published procedures to extract orthologous groups from phylogenetic trees do not allow identification of orthology at various levels of resolution, nor do they document the relations between the orthologous groups. Results: We introduce "levels of orthology" to describe the multi-level nature of gene relations. This is implemented in a program LOFT (Levels of Orthology From Trees) that assigns hierarchical orthology numbers to genes based on a phylogenetic tree. To decide upon speciation and gene dupli...

• Type: Journal
• Year: 2007
• Where: BMCBI
• Authors: René T. J. M. van der Heijden, Berend Snel, Vera van Noort, Martijn A. Huynen
• Keywords: BMCBI 2007, Orthologous Groups, Orthology, Phylogenetic Relations