Peter Rice pmr at sanger.ac.uk
Mon Oct 2 07:38:44 EST 1995

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.
Peter Rice                           | Informatics Division
E-mail: pmr at sanger.ac.uk             | The Sanger Centre
Tel: (44) 1223 494967                | Hinxton Hall, Hinxton,
Fax: (44) 1223 494919                | Cambs, CB10 1RQ
URL: http://www.sanger.ac.uk/~pmr/   | England

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