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A GBrowse plugin written by Joey Bullard and presented by Joan Pontius at the September 2010 GMOD Meeting.

Two GBrowse plugins were presented that were designed by Joey Bullard, an undergraduate student at RIT, and a summer student at the Laboratory of Genomic Diversity in Frederick Maryland under the direction of Joan Pontius. CpG islands in mammalian genomes are often an indication of a well conserved region, such as those of genes and promoter regions. ShortTandemRepeats are useful in experiments for mapping phenotypes to a genetic locus.
Finds total number of CG dimers in a window (default size of 400 bp) and also calculates the expected number of CG dimers based on the basepair composition of the window. A "segments" glyph is used to display the CpG islands, with the height of the glyph representing the number of CG dimers, and the color representing the ratio of observed counts to expected.
A plugin that uses the segments glyph to show Short Tandem Repeats, 2mer-5mers occurring in tandem a minimum of 5 times. The user can configure the number of tandem repeats.

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current21:47, 15 October 2010 (4 KB)Clements (Talk | contribs)
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