software for chromatine ImmunoPrecipitation

Kevin Karplus karplus at cc01.cse.ucsc.edu
Tue Sep 21 12:46:21 EST 2004


In article <I1T8VN$17A5076A39F6E2B3D70D6295986D46A9 at laposte.net>, 
florent crepineau wrote:
> I am involved in the analysis of sequences obtained after
> CHromatin ImmunoPrecipitation (CHIP) in the mouse.
> Thoses sequences are short chromosomal sequences (200bp). What
> I am looking for is a software that would blastN the
> sequences, get the chromosomal location and identify the
> nearest genes and retrieve a longer sequence so I can look for
> transcription factor binding sites.
> 
> Does that exist ?

I believe that the the browser at genome.ucsc.edu can do what you
want, using the BLAT page.  You can search the mouse genome or any of
15 other eukaryotes.  The web server is limited to doing 25 sequences
at a time, but if you have a large number, you could talk with the
researchers in the genome group at UCSC for more direct access.

The browser will not only bring up the context of your sequence, but
also highlight conserved regions and (I think) search for known
transcription factor binding sites.  I don't do DNA myself (I'm in
protein-structure prediction), so I don't use the browser much, and am
not up-to-date on its many features.

(If you are paranoid about your sequences getting out, then you could
download BLAT and the mouse genome, but you have to be pretty paranoid
to do that rather than use the web server---duplicating everything on
the web service and keeping it up-to-date is probably a full time
job---possibly for more than one person.)


------------------------------------------------------------
Kevin Karplus 	karplus at soe.ucsc.edu	http://www.soe.ucsc.edu/~karplus
life member (LAB, Adventure Cycling, American Youth Hostels)
Effective Cycling Instructor #218-ck (lapsed)
Senior member, IEEE	Board of Directors, ISCB (starting Jan 2005)
Professor of Biomolecular Engineering, University of California, Santa Cruz
Undergraduate and Graduate Director, Bioinformatics
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