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Bioinformatics Vol. 18 no. 1 2002
Pages 92-99
© 2002 Oxford University Press

Automated ortholog inference from phylogenetic trees and calculation of orthology reliability

Christian E. V. Storm and Erik L. L. Sonnhammer

Center for Genomics and Bioinformatics, Karolinska Institutet, S-171 77 Stockholm, Sweden

Received on February 2, 2001 ; revised on July 17, 2001 ; accepted on August 15, 2001

Motivation: Orthologous proteins in different species are likely to have similar biochemical function and biological role. When annotating a newly sequenced genome by sequencehomology, the most precise and reliable functional information can thus be derived from orthologs in other species. A standard method of finding orthologs is to compare the sequence tree with the species tree. However, since the topology of phylogenetic tree is not always reliable one might get incorrect assignments.

Results: Here we present a novel method that resolves this problem by analyzing a set of bootstrap trees instead of the optimal tree. The frequency of orthology assignments in the bootstrap trees can be interpreted as a support value for the possible orthology of the sequences. Our method is efficient enough to analyze data in the scale of whole genomes. It is implemented in Java and calculates orthology support levels for all pairwise combinations of homologous sequences of two species. The method was tested on simulated datasets and on real data of homologous proteins.

Availability: Downloadable free of charge from ftp://ftp.cgb.ki.se/pub/prog/orthostrapper/or on request from the authors.

Contact: christian.storm{at}cgb.ki.se


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