In article <mcgorry-1710961340530001 at quadra950.pathology.pitt.edu>,
mcgorry at med.pitt.edu (Michael C. Gorry) wrote:
> We are interested in searching specific sequence data bases (an example
> would be haemophilus influenzae) for short sequences (say TA repeats).
> Is anyone aware of a method/program that could be used to perform such a
search?
The GCG program "findpatterns" is the best way to search for defined
patterns of nucleotides or aminoacids.
Alternatively you could screen out simple repeats from the sequence using
something like XNUN (ftp://ibc.wustl.edu/pub/states/xnun.tar.gz) then scan
through your sequence looking for runs of N's.
Jeffrey Keen
j.keen at ucl.ac.uk
