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looking for cis-elements in the promoter


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6 replies to this topic

#1 vecttoraz

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Posted 11 March 2013 - 10:43 AM

Hi,
Tess is out of service.
I will be very glad if anyone could suggest me another program for searching transcription factors binding sites in a promoter region.
thanks in advance
vecttoraz

#2 pcrman

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Posted 11 March 2013 - 12:31 PM

Here are some tools for analyzing TF binding sites: http://www.protocol-...arch/index.html

#3 vecttoraz

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Posted 11 March 2013 - 12:51 PM

thanks pcrman Posted Image

#4 vecttoraz

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Posted 19 March 2013 - 11:49 AM

Dear PCRman,

I search for TF binding sites with the tools you suggested but I get different results with the different programs. Which one should I believe, I mean to perform CHIP analysis ?

thanks in advance

#5 doxorubicin

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Posted 19 March 2013 - 12:37 PM

I don't know how accurate it is, but this tool is very easy to use: http://www.sabioscie...ch.php?app=TFBS

#6 vecttoraz

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Posted 21 March 2013 - 03:27 PM

Dear Dexorubicin,

thanks, but that site only indicate known promoters.

My task is: I have a promoter region that is polimorphic. Some of these polimorphisms may lead to the binding of different TFs. I want to which putative TFs to performe CHIP however i do not know which tool is more realible in the prediction...

do you have any suggestion.
Thanks very much!!!!!
all the best

#7 doxorubicin

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Posted 22 March 2013 - 04:25 AM

I've been told that TRAP (TRanscription factor Affinity Prediction) is particularly good:
http://trap.molgen.m...gi-bin/home.cgi

Also, I think your assessment of that sabiosciences tool is correct. Based on the description they give, the output is based on their proprietary text mining application. It is strange that when you click on the "View More Transcription Factors" buttion you get 50+ transcription factors with predicted binding sites. I imagine there is some degree of prediction involved.




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