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Visualizing Haplotype Blocks
Ben Fry
MIT Media Lab
Project Description:
When comparing the genome of two different people, you'll see single letter changes (called SNPs, pronounced "snips") every few thousand letters. An interesting feature of SNPs is that their ordering has distinct patterns, where sets of consecutive changes are most often found together. There are many methods for looking at this data, so this piece combines several of them into a single visual display.

The program developed by Ben Fry takes a set of data as input, and can either run as a java applet to show the representation in a web browser, or output it to postscript format for high-resolution rendering. The images show SNP data taken from 500 distinct people, and then broken into 11 clusters based on sets of SNPs that seemed to change as a group. For each of the clusters, there are patterns to the connections between them and their adjacent clusters.

Blocks of related SNPs are grouped together, with the percentage of each particular grouping being depicted by the heights within the individual blocks. For each block, the gray lines between connect a sequence of letters with the sequence found in the next block. The thickness of the gray lines is based on the percentage of how often the two blocks are found adjacent one another. Using an isometric projection, each block is brought out slightly in the z-axis to provide a little extra room between the blocks that are found with little data between them.

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