Bidirectional best hit r-window gene clusters

Background: Conserved gene clusters are groups of genes that are located close to one another in the genomes of several species. They tend to code for proteins that have a functional interaction. The identification of conserved gene clusters is an important step towards understanding genome evolution and predicting gene function. Results: In this paper, we propose a novel pairwise gene cluster model that combines the notion of bidirectional best hits with the r-window model introduced in 2003 by Durand and Sankoff. The bidirectional best hit (BBH) constraint removes the need to specify the minimum number of shared genes in the r-window model and improves the relevance of the results. We design a subquadratic time algorithm to compute the set of BBH r-window gene clusters efficiently. Conclusion: We apply our cluster model to the comparative analysis of E. coli K-12 and B. subtilis and perform an extensive comparison between our new model and the gene teams model developed by Bergeron ...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Melvin Zhang, Hon Wai Leong
• Keywords: BMCBI 2010, Cluster Model, Gene Cluster, Model