Prokaryotic Promoter scanning

John Hartman john at CBI1.CBI.COM
Mon Nov 18 12:27:53 EST 1996


We did a project a few years ago in which a neural network approach was
applied to the prokaryotic promoter problem. The results were pretty
decent,
especially considering that it was only a 6-month project that was
really
focused on massively parallel implementations of neural nets for
sequence
analysis applications, and this was just a test case. It was fun to
watch
the hidden layer activate at the "-35" and "-10" conserved regions,
anyway.
What's particularly cool is that if you use a network with a single unit
in
the hidden layer, you can pretty much read the consensus sequence (and,
I
suppose, derive a detection matrix) from the activation of that hidden
unit
as the sequence is shifted over the inputs.

Alas, it was a Phase I SBIR project that didn't win Phase II funding.

Anyway... for a matrix-oriented approach, see:

   Schneider, Stormo, Gold, and Ehrenfeucht, J.Mol.Bio. 188, 415 (1986).

I think this was their log-odds matrix for the "-10" region:

	A	-2.76	 1.82	 0.06	 1.23	 0.96	-2.92
	C	-1.46	-3.11	-1.22	-1.00	-0.22	-2.21
	G	-1.76	-5.00	-1.06	-0.67	-1.06	-3.58
	T	 1.67	-1.66	 1.04	-1.00	-0.49	 1.84

I don't have the "-35" region matrix handy, though. As I recall, the
actual
distance between the -10 and -35 signals can vary a bit, so be sure to
apply
the two matrices separately.

Happy Hunting!

John

============================================================================
John R. Hartman                                     E-mail: john at cbi.com
Computational Biosciences, Inc.                      Voice:
(313)426-9050
P.O. Box 2090                                          Fax:
(313)426-5311
Ann Arbor, Michigan  48106
============================================================================




More information about the Bio-soft mailing list