CGAT: a comparative genome analysis tool for visualizing alignments in the analysis of complex evolutionary changes between clos

Background: The recent accumulation of closely related genomic sequences provides a valuable resource for the elucidation of the evolutionary histories of various organisms. However, although numerous alignment calculation and visualization tools have been developed to date, the analysis of complex genomic changes, such as large insertions, deletions, inversions, translocations and duplications, still presents certain difficulties. Results: We have developed a comparative genome analysis tool, named CGAT, which allows detailed comparisons of closely related bacteria-sized genomes mainly through visualizing middle-to-large-scale changes to infer underlying mechanisms. CGAT displays precomputed pairwise genome alignments on both dotplot and alignment viewers with scrolling and zooming functions, and allows users to move along the pre-identified orthologous alignments. Users can place several types of information on this alignment, such as the presence of tandem repeats or interspersed r...

• Type: Journal
• Year: 2006
• Where: BMCBI
• Authors: Ikuo Uchiyama, Toshio Higuchi, Ichizo Kobayashi
• Keywords: Alignment Calculation, BMCBI 2006, Genomic Changes, Numerous Alignment Calculation