[Genome] Download Restriction Enzyme Site Coordinates from Human Genome

[K-T Varley]

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: