[Genome] Download Restriction Enzyme Site Coordinates from Human Genome

[Robert Kuhn]

Hello K-T,

Here is the answer to a question similar to yours that describes
how to download and genrate the restriction enzyme data you requested:

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

best wishes,

			--b0b kuhn
			ucsc genome bioinformatics group

> From genome-bounces at soe.ucsc.edu  Fri Jan 25 13:53:19 2008
> To: K-T Varley <kevarley at artsci.wustl.edu>
> Cc: genome <genome at soe.ucsc.edu>
> Subject: Re: [Genome] Download Restriction Enzyme Site Coordinates from
>  Human Genome
> 
> Hello K-T,
> 
> 	The restriction enzyme track is created on the fly, so it's not 
> possible for you to directly create those files yourself using our 
> on-line tools.  However, if you only want one enzyme on one assembly, 
> I'm sure one of our developers would be willing to crank those files out 
> for you.  Please let me know if you would like all locations of TaqI on 
> the hg17 assembly.
> 
> Regards,
> 
> ----------
> Ann Zweig
> UCSC Genome Bioinformatics Group
> http://genome.ucsc.edu
> 
> 
> 
> 
> 
> K-T Varley wrote:
> > Hi,
> > 
> > I want to download a list of coordinates for certain restriction
> > enzyme sites across the human genome, 1 file per chromosome.
> > 
> > If I go to a small coordinate region in the human genome browser I can
> > get the Restr Enzymes track Full display to show the sites of interest
> > in the browser. Then, if I click on one of the sites, I have this
> > option: "Download BED of enzymes in this browser range:  all enzymes,
> > just TaqI".
> > That is great. I want the TaqI BED text file. However, I want it for
> > the whole chromosome, not just a small browser range, but when I zoom
> > out I loose the option to click on that track, and so I don't get the
> > page with the BED file.
> > 
> > How can I get a BED text file of restriction enzyme site coordinates
> > for a particular enzyme and 1 file per chromosome.
> > Thanks for your help!
> > K-T
> > 
> > 
> > 
> > Previous message: [Genome] help with restriction enzyme analysis
> > Next message: [Genome] mRNA mapping-info/coordinates
> > Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
> > 
> > --------------------------------------------------------------------------------
> > 
> > Hello, again, Steve,
> > 
> > One our engineers has generated a file for you that contains the
> > coordinates for all the AclI sites in the hg17 genome sequence.
> > The coordinates are in bed format, representing the six bases of
> > the AclI sites.
> > 
> > To generate a bed file of the type you'd need, you will have to
> > write a script that compares consecutive values for the size
> > you need and combine them into a single record if they are the
> > right size.  E.g., these two adjacent records represent a fragment
> > of 677 bases.
> > 
> > chrY    18618   18624   AclI    0       +
> > chrY    19289   19295   AclI    0       +
> > 
> > The combined entry with the full AclI site on the ends would be:
> > 
> > chrY    18618   19295   AclI    0       +
> > 
> > If you parse the list and make a Custom Track bed file, you can
> > use the browser to get the full fragment sequence.
> > 
> > the file can be found at:
> > _______________________________________________
> > Genome maillist  -  Genome at soe.ucsc.edu
> > http://www.soe.ucsc.edu/mailman/listinfo/genome
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
> http://www.soe.ucsc.edu/mailman/listinfo/genome
>