[Fwd: software for chromatine ImmunoPrecipitation]

florent crepineau florentcrepineau at yahoo.fr
Tue Sep 21 12:46:21 EST 2004


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
> 
> 
> 	
> 
> 	
> 		
> Vous manquez d’espace pour stocker vos mails ? 
> Yahoo! Mail vous offre GRATUITEMENT 100 Mo !
> Créez votre Yahoo! Mail sur
> http://fr.benefits.yahoo.com/
> 
> Le nouveau Yahoo! Messenger est arrivé ! Découvrez
> toutes les nouveautés pour dialoguer instantanément
> avec vos amis. A télécharger gratuitement sur
> http://fr.messenger.yahoo.com
> ---
> 
>  


	

	
		
Vous manquez d’espace pour stocker vos mails ? 
Yahoo! Mail vous offre GRATUITEMENT 100 Mo !
Créez votre Yahoo! Mail sur http://fr.benefits.yahoo.com/

Le nouveau Yahoo! Messenger est arrivé ! Découvrez toutes les nouveautés pour dialoguer instantanément avec vos amis. A télécharger gratuitement sur http://fr.messenger.yahoo.com
---




More information about the Bio-soft mailing list