DNA pattern libraries

Michael Coyne mjcoyne at warren.med.harvard.edu
Tue Aug 2 11:22:56 EST 1994


In article <kofoid-280794123119 at ls-14.biology.utah.edu>,
kofoid at biology.utah.edu (Eric Kofoid) wrote:

> I am hunting for pattern or profile libraries of nucleic acid features
> (promoters, transcriptional stops, ribosome binding sites, etc.) which can
> be used with GCG programs such as FINDPATTERNS and PROFILESEARCH. Please
> reply to the group, as I think this is of general interest.
> 
> Cheers,
> 
> Eric.
> 
> __________________________________________________
> kofoid                     --- close to the truth,
>                            --- far from the sea
> __________________________________________________

I, too, am hunting for such a thing.  I would be very interested in any
replies you might get -- I scan this newsgroup (which doesn't seem to have
much traffic), but if you get any replies via e-mail, I hope you'll share
them.

There was a thread on the bionet.molbio.methds-reagnts by someone looking
for a database of transcription factor binding sequences.  Apparently,
there is a database(s) maintained at NCBI (ncbi.nlm.nih.gov) which may be
what you're (we're) looking for.  The description in the reply described a
SITES database, available in many formats (GCG, FASTA, etc.) in the
/repository/databses directory.

I haven't had a chance to check it out (just picked up the methds-reagnts
thread yesterday), but it might be helpful.

Let me know if you trip over any other hot leads...

Mike
mjcoyne at warren.med.harvard.edu




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