SNPs in Promoter regions

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transplantguy
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SNPs in Promoter regions

Post by transplantguy » Sun Apr 18, 2010 11:40 am

I am new to this so any advice is much appreciated. I am trying to find an easy way to look for SNPs specifically in the promoter regions. Is there any other way apart from cross referencing various databases.

Thanks in advance

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JackBean
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Post by JackBean » Sun Apr 18, 2010 11:49 am

so, you're basically looking for conserved residues in promotors, right?
http://www.biolib.cz/en/main/

Cis or trans? That's what matters.

transplantguy
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Post by transplantguy » Sun Apr 18, 2010 8:50 pm

I guess so, although I am not quite sure what you mean. ENSEMBL has a good way of highlighting SNPs and I presume that bits without variation are the conserved residues you mean

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JackBean
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Post by JackBean » Sun Apr 18, 2010 9:01 pm

Yeah, the CBS at DTU has program for looking for promotor sites
http://www.biolib.cz/en/main/

Cis or trans? That's what matters.

transplantguy
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Post by transplantguy » Mon Apr 19, 2010 10:00 pm

I had a look, seems very complicated and the program only looks for specific promoters. What do you think of looking at say 500 base pairs upstream in Ensembl (which is what I am doing). Thanks for the advice, I will read into that website further.

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