DNA motifs (does a searchable database exist)

Harry Mangalam mangalam at uci.edu
Wed Nov 2 13:31:21 EST 1994


In article <m_cockerill-2710942044070001 at timpwrmac.clh.icnet.uk>,
m_cockerill at icrf.icnet.uk (Matthew Cockerill) wrote:

> I'm wondering whether there is any analogue of PROSITE which catalogs DNA
> motifs (e.g. transcription factor binding sites, promoter consensus 
> sequences, 3'UTR mRNA masking signals, things like that, which occur in
> non coding regions of DNA).
> 
> Seem it would be very useful.
> Consensus sequences for thousands of these type of motifs are present in
> the literature. Has anyone assembled them in searchable form?

Hi Matt,
   Well, there's Ghosh' Transcription Factor Database
(ftp://ncbi.nlm.nih.gov/repository/TFD) which contains much of what you're
looking for, and you could agrep (approximate grep, with regular
expresssion search) thru  it for hits or make up a perl script to do more
in one pass.

Cheers
harry

-- 
  Harry J Mangalam, Microbiology and Molecular Genetics, 
    College of Medicine, UC Irvine, Irvine, CA, 92717, 
         (714) 856-4824, fax (714) 856 8598,
 --- That which does not kill me, makes me grouchier ---
         http://hornet.mmg.uci.edu/~hjm/hjm.html
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