Speaker: Xin He is a graduate student in the Department of Computer Science. He is working with Prof. Bruce Schatz and Chengxiang Zhai on bioinformatics and computational biology. Title: Identifying Conserved Gene Clusters in the Presence of Homology Families Abstract: This talk is based on a paper that will published in Journal of Computational Biology, Special Issue of RECOMB2004. The study of conserved gene clusters is important for understanding the forces behind genome organization and evolution, as well as the function of individual genes or gene groups. In this talk, I will present a model and algorithm for identifying conserved gene clusters from pairwise genome comparison. This generalizes a recent model called “gene teams”. A gene team is a set of genes that appear homologously in two or more species, possibly in a different order yet with the distance of adjacent genes in the team for each chromosome always no more than a certain threshold. We remove the constraint in the original model that each gene must have a unique occurrence in each chromosome, and thus allow the analysis on complex prokaryotic or eukaryotic genomes with extensive paralogs. Our algorithm analyzes a pair of chromosomes in O(mn) time and uses O(m + n) space, where m and n are the number of genes in the respective chromosomes. We demonstrate the utility of our methods by studying two bacterial genomes, E. coli K-12 and B. subtilis. Many of the teams identified by our algorithm correlate with documented E. coli operons, while several others match predicted operons, previously suggested by computational techniques. Our implementation and data are publicly available at http://euler.slu.edu/~goldwasser/homologyteams/. Related Link:
https://netfiles.uiuc.edu/xinhe2/www/JCB.pdf
https://netfiles.uiuc.edu/xinhe2/www/RECOMB2004.pdf
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