finding short DNA motifs

Oliver Hobert hobert at FRODO.MGH.HARVARD.EDU
Fri Jul 26 20:26:31 EST 1996

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.

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

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