Skittle: uma ferramenta de visualização do genoma bidimensional

Skittle: A 2-Dimensional Genome Visualization Tool

Josiah D Seaman*1 and John C Sanford2

Address: 1FMS Foundation, 7160 Stone Hill Rd., Livonia, NY 14487, USA and 2Dept. Hort. Sci., NYSAES, Cornell University, Geneva, NY 14456,
USA

Email: Josiah D Seaman* - Josiah.D.Seaman.1@ohio.edu; John C Sanford - jcs21@cornell.edu

* Corresponding author

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 allowsthe 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.

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NOTA DESTE BLOGGER:

Mais e mais complexidade genômica será revelada através de pesquisas utilizando o Skittle. Quem viver verá o que Darwin, limitado pela limitação tecnológica do seu tempo, não pode ver. Tivesse, será que teria elaborado a teoria da evolução através da seleção natural? Darwin não explica nem o flagelo bacteriano, quanto mais a origem e evolução da diversidade e complexidade da vida.

Fui, nem sei por que, pensando que a montanha de evidências a favor do fato, Fato, FATO da evolução a cada dia que passa mais se parece com uma baita miragem epistêmica...

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