From owner-celegans@net.bio.net Fri Jul 26 23:00:00 1996
Path: biosci!FRODO.MGH.HARVARD.EDU!hobert
From: hobert@FRODO.MGH.HARVARD.EDU (Oliver Hobert)
Newsgroups: bionet.celegans
Subject: finding short DNA motifs
Date: 26 Jul 1996 18:26:31 -0700
Organization: BIOSCI International Newsgroups for Molecular Biology
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Does anybody know how to find out how often a short given DNA sequence (for
example a transcription factor binding motif) can be found in the C.elegans
genome ? How about a permutet sequence, for example how often does
A-A-C/A-G-C exist ?
Blasting the database with short sequences does not give any results.
Knowing how to do that would allow analysing promoter regions of favorite
genes for consensus binding motifs and - provided some are found - to
assess how statistically significant the existence of such a binding site
is, meaning how likely it is that in a let's say 3 kB promoter this site
just appears by chance.
TX,
Oliver

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Oliver Hobert
Harvard Medical School/Department of Genetics
Mass. General Hospital/Department of Mol. Biol.
Ruvkun-Lab
Wellman 8
Boston, MA 02114
Fax: 1-617-726 6893
Tel: 1-617-726 5983
e-mail: hobert@molbio.mgh.harvard.edu
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