Identifying Conserved Gene Clusters in the Presence of Homology Families

by Xin He and Michael H. Goldwasser


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 paper, we present a new 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

Identifying Conserved Gene Clusters in the Presence of Homology Families
Xin He and Michael H. Goldwasser,
Journal of Computational Biology, 12(6):638--656, 2005.
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A preliminary version originally appeared as:
Identifying Conserved Gene Clusters in the Presence of Orthologous Groups
Xin He and Michael H. Goldwasser
Proceedings of the Eighth Annual International Conferences on Research in Computational Molecular Biology (RECOMB), San Diego, California, Mar. 2004, pp. 272-280.
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Michael H. Goldwasser