[bip] online sites for doing binding site search

[Erich Schwarz]

On Thu, 29 Nov 2007, Titus Brown wrote:

> ...  I'm writing a short review/HOWTO on finding cis-regulatory
> elements in chick ...

    My own jaundiced view is that there is no particularly good
search tool out there yet.  Of course, that means opportunity! for
those of us trying to make better search tools...

    However, I just re-read this article on cis-regulatory
analysis by Wasserman and Sandelin, which may be worth passing
on:

    http://www.nature.com/nrg/journal/v5/n4/full/nrg1315.html

Wasserman himself is involved with these sites:

    http://www.oreganno.org
    http://nar.oxfordjournals.org/cgi/content/full/gkm967v1

    http://www.pazar.info
    http://genomebiology.com/2007/8/10/R207

    http://www.cisreg.ca/oPOSSUM/
    http://nar.oxfordjournals.org/cgi/content/full/35/suppl_2/W245

as well as with JASPAR.


--Erich