In article <Pine.OSF.3.91.950929102436.24326C-100000 at diamond.tufts.edu> Sanjay Krishnaswamy <skrishna at diamond.tufts.edu> writes:
> Is there a tool in GCG 8.0 which will enable me to find Shine-Dalgarno
> sequences or prokaryotic promoter regions?
You have a choice, depending on how much work you want to do.
You could search for a simple short pattern, with mismatches, and get
*a lot* of false hits.
You could also make a profile for the Shine-Dalgarno and promoter regions
of the species you work with, and use the profile analysis programs.
I have done this successfully with GCG 7.x for E.coli promoters.
I guess I still have the original sequence alignment around somewhere.
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