software for chromatine ImmunoPrecipitation

Malay mbasu at mail.nih.gov
Tue Oct 5 11:28:14 EST 2004

Kevin Karplus wrote:
> 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.)
You can use netblast client of NCBI. To search against a genome use the 
databases listed in the doc. It works just like the local blast but does 
the search on NCBI server.


Malay K Basu
mbasu at ncbi.nlm.nih.gov

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