[BioC] DNA, not RNA: motif mining

[Harry Mangalam]

There are lots of such tools, both to search known databases or to search for 
self-described patterns.

The following link shows lots of such ones.

http://bip.weizmann.ac.il/bio_tools/dna-tools.html

If you're going to search genomic sized chunks, a program I wrote called 'tacg' 
is pretty good and searches for IUPAC patterns (with or without errors), regular 
expressions, matrix descriptions, as well as for windows satisfying rules for 
the above:

  ((pattern A AND pattern B) NOT (Pattern C AND pattern D)) XOR (Pattern E NOT 
PAttern F)) in a sliding window of 1500 bases.

for example.

Described in more detail at:
http://www.biomedcentral.com/1471-2105/3/8

Lemme know if you want the latest version. Runs on linux, MacOSX, Solaris, 
probably other *nixs

hjm



Johnnidis, Jonathan wrote:
> 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
> 
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-- 
Cheers, Harry
Harry J Mangalam - 949 856 2847 (vox; email for fax) - hjm at tacgi.com
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