Motif enrichment

[k-gun12]

I have a degenerate motif, i.e AMNCDAYMNNTCA that I find clustered several times within 200bp of a 9kb contig. I need to test for enrichment there and qualify the likelihood of that happening (i.e six times in 200bp of seven total occurrences in 9kb of sequence). Does anyone have a suggestion for a tool that will give a probability? I'm trying to show functional enrichment...

Thanks!

[dpryan]

The simplest method would be to just calculate the number of occurences of this pattern per sliding 9kb window (or 200bp on either side of it, I suppose), excluding those region of interest and/or those overlapping them. This then becomes the background distribution. You can then perform a wilcoxon test between the two distributions. This method makes some assumptions about the properties of the contigs, namely that they were defined using a method that can sample the genome uniformly (i.e., these aren't defined by an NGS or array-based experiment). If your genome has a bunch of Ns anywhere, then you probably want to exclude those regions.