Web-based visualization tools for bacterial genome alignments

摘要: With the increase in flow of sequence data, both contigs and whole genomes, visual aids for comparison analysis studies are becoming imperative. We describe three web-based tools visualizing alignments bacterial genomes. The first, called Enteric, produces a graphical, hypertext view pairwise between reference genome sequences from each several related organisms, covering 20 kb around user-specified position. Insertions, deletions rearrangements relative to color-coded, which reveals many intriguing differences among second, Menteric, computes displays nucleotide-level multiple same sequences, together with annotations ORFs regulatory sites, 1 region surrounding given address. third, Java-based viewer Maj, combines some features previous tools, adds zoom-in mechanism. compare Escherichia coli K-12 partially sequenced genomes Klebsiella pneumoniae, Yersinia pestis, Vibrio cholerae, Salmonella enterica serovars Typhimurium, Typhi Paratyphi A. Examination allows one draw inferences about patterns functional assignments. For example, these revealed that rffH, gene involved enterobacterial common antigen (ECA) biosynthesis, is partly deleted used PCR show this deletion occurs sporadically strains S.enterica subspecies I but not any tested six other subspecies. resulting cell surface diversity may be associated selection by host immune response.