Bioinformatics Vol. 18 no. 90001 2002
Pages S276-S284
© 2002 Oxford University Press
A tree kernel to analyse phylogenetic profiles
Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto, 611-0011, Japan
Received on January 24, 2002
; revised on March 26, 2002
; accepted on March 26, 2002
Motivation: The phylogenetic profile of a protein is a string that encodes the presence or absence of the protein in every fully sequenced genome. Because proteins that participate in a common structural complex or metabolic pathway are likely to evolve in a correlated fashion, the phylogenetic profiles of such proteins are often ‘similar’ or at least ‘related’ to each other. The question we address in this paper is the following: how to measure the ‘similarity’ between two profiles, in an evolutionarily relevant way, in order to develop efficient function prediction methods?
Results: We show how the profiles can be mapped to a high-dimensional vector space which incorporates evolutionarily relevant information, and we provide an algorithm to compute efficiently the inner product in that space, which we call the tree kernel. The tree kernel can be used by any kernel-based analysis method for classification or data mining of phylogenetic profiles.
As an application a Support Vector Machine (SVM) trained to predict the functional class of a gene from its phylogenetic profile is shown to perform better with the tree kernel than with a naive kernel that does not include any information about the phylogenetic relationships among species. Moreover a kernel principal component analysis (KPCA) of the phylogenetic profiles illustrates the sensitivity of the tree kernel to evolutionarily relevant variations.
Availability: All data and software used are freely and publicly available upon request.
Contact: Jean-Philippe.Vert{at}mines.org
Keywords: phylogenetic profile; tree; kernel; support vector machine; gene function prediction.
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