The Skittle Genome Browser provides powerful data visualizations that allow humans and computers to do what they are best at, respectively. Each data visualization is a mathematical trans­form that creates an image from the raw sequence data designed to make some aspect of the sequence intuitive to human pattern recognition. Skittle's unique approach presents the raw data to the user without biasing assumptions about what the sequence contains such as arbitrary thresholds or filters.

For example: the Nucleotide Display transforms four characters (ACTG) into four colors. Browsing several human chromosomes reveals abrupt changes in nucleotide usage bias (isochores) which are present at even small scales (less than one kilobase). This creates a vis­ually interesting pattern that you can interactively browse. Another visualiza­tion, the Repeat Map graph, shows all possible repeats in a given region--everything from ATAT repeats to seg­mental duplications are presented on a single screen.

Skittle is an entire toolset of graphs each with their own strength. Used in combination, they create a powerful re­search tool that you can use to quickly characterize a genetic sequence without any previous knowledge or any assump­tions that would cause you to miss important discoveries.

It is well known that the human mind excels at pattern recognition (e.g., near-instantaneous face recognition), but the mind needs graphical help when dealing with large amounts of numerical data. There is currently a lack of tools available for general genomic visual­ization. Several abstract tools do exist, but we felt a need for the introduction of a simple tool that is optimized for the visualization of genomic data specifically. The primary goal in the development of Skittle was to give the user the simplest possible way to visually examine raw genomic data.

Skittle was not designed to compete with pre-programmed single purpose algorithms already in existence. Cur­rently available research tools require you to already know what you are looking for before you begin. With Skittle, you can characterize a chromo­some from a more unbiased starting point. Then once you know the major features you can tailor algorithms and use other tools to fully quantify your discoveries. Using Skittle means that you can learn things you didn't know about your subject. This approach is complementary to existing tools.

• Miniature chromosome structure implanted in Human Y chromosome (whole structure, degraded centromere, bottom telomere, top telomere)
• Frequent Triplex binding sites can be seen everywhere in the genome (Example 1, Example 2, Example 3)
• A 125bp tandem repeat with over 2,000 copies
• Tandem repeats often have structured variation in their nucleotide substitution (Example 1, Example 2, paper)
• Computer program code also has tandem repeats with the same kind of variation patterns [in publication]
• The Alu distributed repeat not only comes in dimer but is often a monomer, trimer, or 4-mer
• Skittle can identify assembly errors. Some large gaps in the human genome sequence are because segmental duplications make assembly difficult. In these cases you can see that the gap is not the correct size because it is not a multiple of the duplicated sequence (Example, Paper)
• Pure Poly-A sequences are found everywhere in the genome
• Physical chromosome territories correlate strongly (0.65) with isochores defined by oligomer usage (Full paper)

DNA Skittle is developed by Newline Technical Innovations based on the original desktop application created by Josiah Seaman. We are excited about this tool and would welcome any opportunity to enhance its capabilities, utility, and adoption.

Email:

info@newline.us

Phone:

719-428-5636

Though Skittle is still in a very early stage of development we are very interested in your feedback and input. If you have encountered a bug or have trouble with any of the features please contact our support team at info@newline.us.