In the newest issue of BMC Bioinformatics 2009 (10:452), Josiah Seaman and John Sanford publish details for their 2-D genome visualizer called ‘Skittle’.
Results: This program first creates a 2-dimensional nucleotide display by assigning four colors to the four nucleotides, and then text-wraps to a user adjustable width. This nucleotide display is accompanied by a “repeat map”which comprehensively displays all local repeating units, based upon analysis of all possible local alignments.
Skittle includes a smooth-zooming interface which allows the user to analyze genomic patterns at any scale.Skittle is especially useful in identifying and analyzing tandem repeats, including repeats not normally detectable by other methods. However, Skittle is also more generally useful for analysis of any genomic data, allowing users to correlate published annotations and observable visual patterns, and allowing for sequence and construct quality control.
Skittle is freely available from their Sourceforge page, and they have a great document with example visualizations in this PDF.
via Skittle: A 2-Dimensional Genome Visualization Tool – 7thSpace Interactive.
