title: Visualization of comparative genomic analyses by BLAST score ratio.
abstract: BACKGROUND
  The first microbial genome sequence, Haemophilus influenzae, was published in 1995. Since then, more than 400 microbial genome sequences have been completed or commenced. This massive influx of data provides the opportunity to obtain biological insights through comparative genomics. However few tools are available for this scale of comparative analysis.
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  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/.
authors.affiliation: The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA. drasko@tigr.org <drasko@tigr.org>
authors.forename: David A
authors.initials: DA
authors.lastname: Rasko
authors.forename: Garry S A
authors.initials: GS
authors.lastname: Myers
authors.forename: Jacques
authors.initials: J
authors.lastname: Ravel
mesh_terms: D000465:Algorithms; D007446:Chromosome Inversion; D019295:Computational Biology / Q000379:methods*; D003196:Computer Graphics; D030541:Databases, Genetic; D017353:Gene Deletion; D016678:Genome; D016680:Genome, Bacterial; D023281:Genomics; D020407:Internet; D010455:Peptides / Q000737:chemistry; D011381:Programming Languages; D040901:Proteomics / Q000379:methods; D016415:Sequence Alignment; D012984:Software; D014584:User-Computer Interface
chemical_list: D010455:Peptides