We identified numerous regions where a specific motif of interest is enriched. We want to see if there is a correlation between these regions and hypervariable regions in the human genome. Is there something easier than manually checking using the genome browser?
Frederic Lepretre
Hi Jean,
depending on the length of your motif, if it's more than 20b you can use a blast and find all the positions at the UCSC website (http://genome.ucsc.edu/cgi-bin/hgBlat?command=start), just be sure to choose the right genome/assembly (I would take the hg19 since the last is not stable yet). if it's lower than 20, you'll need to download the genome and by command line search with a grep all you're waiting for.
fred
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