[Bioc-sig-seq] Using library(cosmo) for motif detection

[Ivan Gregoretti]

Hello fellow bioconductorians

One common question that arises after a successful ChIP-seq peak
detection is "What is the binding motif"?

The package cosmo was created to answer that question. The
documentation shows a very nice example to get you started when you
know what your binding site should look like.


This is my question to cosmo experts

--How do you start when you have no a priori knowledge, not even the
length of the motif?

I expect to go through several iterations but the question still
stands: all I know is that this mysterious transcription factor binds
to DNA rather than Martian rocks.

Thank you,

Ivan


Ivan Gregoretti, PhD
National Institute of Diabetes and Digestive and Kidney Diseases
National Institutes of Health
5 Memorial Dr, Building 5, Room 205.
Bethesda, MD 20892. USA.
Phone: 1-301-496-1016 and 1-301-496-1592
Fax: 1-301-496-9878