You may want to take a look at MEME http://www.sdsc.edu/MEME/meme/website/
HMMs can also be used to find and model motifs, but neither of the two
HMM packages (HMMer http://genome.wustl.edu/eddy/hmm.html and
SAM http://www.cse.ucsc.edu/research/compbio/sam.html) is as highly
optimized for motif search.
Richard
In article <5rqbt7$1vb$1 at news.fas.harvard.edu>, remeans at fas.harvard.edu (Robert Means) writes:
|> Hello,
|> I'm trying to find (and hopefully not have to write!) some
|> software that will let me take multiple a.a. sequence alignments and then
|> look for specific protein motiffs and generate statistics about the
|> number of sequences containing the motiff at a certain location. Is there
|> anything like this out there. It seems like some of the alignment programs
|> take structure and motiffs into consideration when doing alignments.
|> Anyway, if I could get some help it would be appreciated.
|> Thanks in Advance,
|> Robert Means
|>REMEANS at husc.havard.edu|>
