Methods of Horizontal Gene Transfer Determination Using Phylogenetic Data

Issue title: 3rd International Conference on Bioinformatics of Genome Regulation and Structure (BGRS 2002), June 2002, Novosibirsk, Russia

Article type: Research Article

Authors: Lyubetsky, Vassily A. | V'yugin, Vladimir V.

Affiliations: Institute for Information Transmission Problems RAS, Moscow, Russia Email: [email protected] | Institute for Information Transmission Problems RAS, Moscow, Russia, Email: [email protected]

Abstract: A new approach for comparative analysis of multiple trees reconstructed for representative protein families is proposed. This approach is based on the hypothesis of gene duplication, gene loss and horizontal gene transfer and makes use of stochastic methods and optimization. We present a species tree of 40 prokaryotic organisms obtained by our algorithm on the basis of 132 clusters of orthologous groups of proteins (COGs) from the GenBank of the National Center for Biotechnology Information (USA). We also present a computer technology intended to determine horizontally transferred genes. Some application results of the technology, based on comparative analysis of protein and species trees, are given.

Keywords: evolution, phylogenetic trees, consensus trees, horizontal gene transfer, mathematical models of evolution, stochastic optimization

Journal: In Silico Biology, vol. 3, no. 1-2, pp. 17-31, 2003