Tools for Discovering Genes Containing a DNA motif

Question

[dk0319]

Can anyone recommend tools for generating a list of genes that contain a DNA motif of interest. Ideally, one that provides a summary statistic. I was able to use MEME to identify a motif from several bed files. Now I would like to generate a list of genes with said motif preferably in the promoter region. I used GOMO to get GO terms and that generates gene IDs but these are not in a convenient format. Cheers

Answer 1

[jared.andrews07]

I'd probably just use FIMO and intersect the output locations with gene promoters (however you want to define that) via bedtools intersect.