Hi Simon Lin,
thank you for the answer. I totaly agree with you that
it is not a trivial problem that is why I contacted
the list because I was fully aware that I could not do
it by myself.
However, I recently found a blast page (unfortunatly,
I don't remember where) where the result was a
chromosome map displayed with the blasted sequence
highlighted, the genes and so on. And to retrieve a
longuer sequence, people doing promoter analysis after
microarray have developed such tool.
Maybe SAGE people have done such a program to identify
SAGE tags and the gene associated?
As usual the different parts of the tool have been
developed but I need someone to get them together to
do what I want ;-)
Best regards
Florent Crepineau
--- Simon Lin <Simon.Lin at duke.edu> a écrit :
> Hi, Florent Crépineau:
>> The problem you described is nothing trivial. You
> really need a
> bioinformatics team (I mean, > 2 persons) to work
> with you!
>> We had a lab at Duke tried to do the same thing by
> hand (they though
> they can!); but finally they gave up. Lab people
> tend to under-estimate
> informatics problems.
>>> Good luck!
>> Simon
>>>> =================================================
> Simon M. Lin, M.D.
> Manager, Duke Bioinformatics Shared Resource
> Assistant Research Professor, Biostatistics and
> Bioinformatics
> Box 3958, Duke University Medical Center
> Rm 286 Hanes, Trent Dr, Durham, NC 27710
> Ph: (919) 681-9646 FAX: (919) 681-8028
> Lin00025 (at) mc.duke.edu
>http://dbsr.duke.edu> =================================================
>>>>
> ATTACHMENT part 2 message/rfc822 name=software for
chromatine ImmunoPrecipitation
> De: florentcrepineau at yahoo.fr (florent crepineau)
> Objet: software for chromatine ImmunoPrecipitation
> Date: 6 Sep 2004 11:46:07 +0100
>> Dear all,
>> 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 ?
>> Best regards
>> Florent Crépineau
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