Visualization of comparative genomic analyses by BLAST score ratio

The BLAST Score Ratio (BSR) approach, implemented in a Perl script, classifies all putative peptides within three genomes using a measure of similarity based on the ratio of BLAST scores. The output of the BSR analysis enables global visualization of the degree of proteome similarity between all three genomes. Additional output enables the genomic synteny (conserved gene order) between each genome pair to be assessed. Furthermore, we extend this synteny analysis by overlaying BSR data as a color dimension, enabling visualization of the degree of similarity of the peptides being compared.Combining the degree of similarity, synteny and annotation will allow rapid identification of conserved genomic regions as well as a number of common genomic rearrangements such as insertions, deletions and inversions. The script and example visualizations are available at: http://www.microbialgenomics.org/BSR/ webcite.In the decade since the publication of the Haemophilus influenzae genome sequence in 1995 [1], 191 microbial genomes have been completed, with another 276 in progress [2]; as of October 14, 2004). Multiple strains of the same organism, or multiple species of the same genus are being sequenced or have been completed, making comparative genomic analysis possible on an unprecedented scale. As the technology continues to improve, the number of completed microbial genome sequences will further increase – a major challenge of the comparative genomic era is to fully exploit this data. However, the development of tools for analysis of such data sets has not kept pace.BLAST analysis has become a ubiquitous method of interrogating new sequence data, but there are limitations to using BLAST alone as a discriminating tool. Many other methods and individuals use BLAST output E-values as a criterion for data parsing. While this measure may be efficient, the output is often skewed by both the database used for comparison and the length of the match [3]. Small regions of high similari