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Open Access Highly Accessed Software

Skittle: A 2-Dimensional Genome Visualization Tool

Josiah D Seaman1* and John C Sanford2

Author Affiliations

1 FMS Foundation, 7160 Stone Hill Rd., Livonia, NY 14487, USA

2 Dept. Hort. Sci., NYSAES, Cornell University, Geneva, NY 14456, USA

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BMC Bioinformatics 2009, 10:452  doi:10.1186/1471-2105-10-452

Published: 30 December 2009

Abstract

Background

It is increasingly evident that there are multiple and overlapping patterns within the genome, and that these patterns contain different types of information - regarding both genome function and genome history. In order to discover additional genomic patterns which may have biological significance, novel strategies are required. To partially address this need, we introduce a new data visualization tool entitled 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.

Conclusions

Preliminary observations using Skittle reveal intriguing genomic patterns not otherwise obvious, including structured variations inside tandem repeats. The striking visual patterns revealed by Skittle appear to be useful for hypothesis development, and have already led the authors to theorize that imperfect tandem repeats could act as information carriers, and may form tertiary structures within the interphase nucleus.