Prokaryotic Promoter scanning

R.C.Ogden bsp041 at thunder
Thu Nov 14 10:26:37 EST 1996


Our lab has now regularly sequences degradative genes (mainly from
Pseudomonas sp.). We would like to identify any upstream regulatory
sequences, or potential regulatory sequences, such as promoters, known
prokaryotic enhancers and regulator binding sites (such as those for LysR
and NtrC regulator families).These seems to be several programs and web
sites offering similar analysis of EUKARYOTIC sequence data but very
little aimed at E.coli and other bacteria.  Can anyone suggest any
resources to scan our upstream sequence ? 

	I know PC Gene will try to identify bacterial promoters but
unfortuneately we do not have access to it. We do have telnet access to a
facility running STADEN which may do the trick, however, the manual seems
to indicate that it requires a matrix to recognise promoters - which I 
can't locate and don't have the knowledge to calculate from 1st 
principles ! Surely there is a need for this sort of analysis, perhaps 
there is a web site some where which is kept up to date with new sequence 
elements etc ? Anyone know of its URL ?

	Any help would be greatly appreciated, DOS, Windows, UNIX or 
on-line. We will take what we can get.

			Cheers & thanks in advance

					Ricbhard

***************************************************************************

 Richard C. Ogden,                      E-mail: r.c.ogden at bangor.ac.uk
 School of Biological Sciences,          Phone: 01248 351151 ext.2368
 University of Wales, BANGOR               Fax: 01248 370731
 LL57 2UW, UK.

Drop in to our Biodegradation Homepage at: 
********* http://oracle.bangor.ac.uk/sbs/research/biodegradation/ *********



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