[Genome] Restriction enzyme sites

[Robert Kuhn]

Kevin,

We do not actually precompute the restriction enzyme sites
for the Genome Browser, but compute them for your browser window 
on the fly.  The table would be too big.  There are actaully three
tracks in the track group you mention that are not underlain
by a table:  Base Position, Short Match and Restriction Enzymes,
though the Re track does refer to a table in the hgFixed database
to get the enzyme cutsite information.

The following mailing list question/answer gives some detail about 
how you might get the information you seek using some of our other 
tools:

  http://www.cse.ucsc.edu/pipermail/genome/2006-May/010707.html

Please note that you can search the mailing list archives using
the middle of the three boxes on this page:

  http://genome.ucsc.edu/contacts.html

Of course, if you do not find what you need there or if the link I
provided does fully answer your question, please contact us again.

thanks,
				--b0b kuhn
				ucsc genome bioinformatics group



> From genome-bounces at soe.ucsc.edu  Wed Oct 11 09:14:55 2006
> To: genome at soe.ucsc.edu
> Subject: [Genome] Restriction enzyme sites
> 
> Hello,
> I am trying to obtain the coordinates for list of restriction enzyme 
> sites for a set of rare cutters across the mouse genome. 
> Specifically, we are interested in a class of homing endonucleases 
> (PI-SceI, PI-PspI, I-CeuI, and I-SceI). I see from the browser view 
> that you can display all sites for a particular region but I can't 
> find the restriction enzyme table in the Table Browser. In the genome 
> browser, the track is listed under the heading "Mapping and 
> Sequencing Tracks" but it doesn't seem available for export. From the 
> log reports, Restriction Enzyme mapping (REbase release 505) is 
> listed as an available table for mm6 Mar. 2005 but I can't seem to 
> find this either when looking under all tracks or all tables.
> 
> If you could please provide some assistance as to the location  of 
> this data and a possible way of obtaining it for the most current 
> mouse build that would be most appreciated. I thought about just 
> BLATing my sequences but the server appears to be down at the moment. 
> Any help you can provide in clearing up this issue would be most 
> appreciated because it seems like it should be fairly straightforward 
> to obtain this data if it can be displayed.
> 
> Thanks!
> Kevin
> -- 
> Kevin A. Peterson
> Graduate Research Assistant
> Department of Biomedical Sciences
> College of Veterinary Medicine
> Veterinary Research Tower T3001 Box 16
> Cornell University
> Ithaca, NY 14853
> 
> kap59 at cornell.edu
> fax: (607) 253-4495
> phone: (607) 253-4122
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