[Genome] Fwd: cool

[Tim Hefferon]

Kate,

I sent these to the general help address earlier, but didn't get a  
response. (Same with the next e-mail.)

Can you please help answer the question? I find myself in need of  
this tool again.

Thanks,
Tim


Begin forwarded message:

> From: Tim Hefferon <timhefferon at gmail.com>
> Date: April 22, 2007 7:23:11 AM GMT-06:00
> To: genome at soe.ucsc.edu
> Subject: cool
>
> Hi,
>
> Jim Kent's Perfect Match to Short Sequence feature is useful.
>
> What would make it extremely useful is if it could search for  
> degenerate matches, using the IUPAC code.
>
> Let's say, for example, that I am interested in finding binding  
> sites for a transcription factor or a splicing factor, whose  
> binding site is AG(Py)TG(Pu). If the feature I request were  
> available, I could simply enter 'AGYTGR' and BANG - there are all  
> the potential binding sites for that protein.
>
> Please ask Jim whether it would be a simple matter to include this  
> feature. As an aside, it would be helpful if, on the page where one  
> enters the sequence to be searched, there were a summary of the  
> IUPAC code for reference.
>
> Thank you!
>
> Tim Hefferon
>
>