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Visualization of comparative genomic analyses by BLAST score ratio.
David A Rasko1, Garry S A Myers, Jacques Ravel
1The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA. drasko@tigr.org <drasko@tigr.org>
BMC Bioinformatics
|January 7, 2005
Summary
A new tool analyzes microbial genomes, comparing protein similarity and gene order to reveal conserved regions and rearrangements. This facilitates deeper insights from the growing volume of genomic data.
Area of Science:
- Microbial genomics
- Bioinformatics
- Comparative genomics
Background:
- Over 400 microbial genomes sequenced since 1995.
- Vast data offers biological insights via comparative genomics.
- Limited tools exist for large-scale comparative analysis.
Purpose of the Study:
- To develop a tool for large-scale comparative genomic analysis.
- To enable visualization of proteome similarity and genomic synteny.
Main Methods:
- Developed a Perl script implementing the BLAST Score Ratio (BSR) approach.
- Classified peptides across three genomes based on BLAST score ratios.
- Assessed genomic synteny and visualized peptide similarity.
Main Results:
- Global visualization of proteome similarity between genomes.
- Assessment of genomic synteny (conserved gene order).
- Overlay of BSR data for visualizing peptide similarity.
Conclusions:
- Combined similarity, synteny, and annotation identify conserved regions and rearrangements.
- Facilitates rapid identification of genomic insertions, deletions, and inversions.
- Tool and visualizations available at http://www.microbialgenomics.org/BSR/