Create BED file with restriction enzyme (HindIII) cutting sites of whole chromosome/genome

Question

[peer_wuensche]

Hi there,

I would like to display HindIII cutting sites in a genome browser. Ideal would be a bed file or something similar, which enables me to upload this to my browser of choice.

Is there any website where I could download such file, or do I have to generate it myself and if so, how?

Any help is highly appreciated!

Best Peer

Answer 1

[Pierre Lindenbaum]

create a BED file from In Silico Genome Digestion ?

[peer_wuensche]

Alright, got a little java 101 lesson from a colleague, and managed to modify the In Silico Genome Digestion to my needs. ...works like a charm. :) Thanks a lot!!

[Pierre Lindenbaum]

cool. You can now validate my answer (flag on the left)

[peer_wuensche]

sure did. ;)

[peer_wuensche]

I saw your post earlier on, but unfortunately I have no clue about Java :/ Any solutions using unix or R or even web-based? Sorry, I am more of a wet-lab biologist.

Answer 2

[jotan]

If you just need a screengrab, you can do this directly in UCSC. Under "Mapping and Sequencing", click on "Restr Enzymes". Type in Hind III (or your RE of choice) and select your display mode.

[peer_wuensche]

I've tried to use this feature before, but it won't give me the information genome wide or let me download the information as a bed file. Thanks anyway for pointing this out!