Assignment 7

Due date: 5/13/13

Detecting and visualizing CpG islands

The CG di-nucleotide is a lot less common in vertebrate genomes than would be expected by chance, with the exception of regions called CpG islands, which tend to occur in promotors (wikipedia has a good article on the topic). Write a function that detects high CG content in a window of size around 500 bp in a genome of interest and plots the CG content in a region surrounding the detected region.

Submit your code, along with the resulting plots via ramct. Please use human chromosome 18 for your analysis, which you can download from from the UCSC genome website.