- Article -
| In Silico Biology 3, 0003 (2003); ©2003, Bioinformation Systems e.V. |
Methods of horizontal gene transfer determination using phylogenetic data
Vassily A. Lyubetsky1 and Vladimir V. V'yugin2,*
Institute for Information Transmission Problems RAS, Moscow, Russia
1Email: lyubetsk@iitp.ru
2Email: vld@vyugin.mccme.rssi.ru
* corresponding author
Edited by E. Wingender; received September 30, 2002; revised and accepted February 22, 2003; published March 16, 2003
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.
Key words: evolution, phylogenetic trees, consensus trees, horizontal gene transfer, mathematical models of evolution, stochastic optimization