[BioC] DNA, not RNA: motif mining

[Johnnidis, Jonathan]

dear BC folks:

I gather most activities in the R/BC community are centered around RNA and the manipulation of expression data. However, in addition I am interested in control sequences in DNA and wonder if there are any tools (within R or another (similar?) environment) that would allow one to search large chunks of sequence for enrichment for any known cis-acting control elements (promoters, enhancers, silencers, repeat elements, MAR's, etc.)?

I'm not sure if this is the appropriate list on which to inquire, but I'd much appreciate any feedback, or direction to another forum.

with thanks,

Jonathan