[EMBOSS] restrict

Mehta, Perdeep Perdeep.Mehta at STJUDE.ORG
Mon Feb 22 23:21:38 UTC 2010


I want to use the "restrict" program in EMBOSS package to do a restriction digest of a nucleotide sequence. When I ran restrict, it threw the following error;

EMBOSS An error in restrict.c at line 147:
Cannot locate enzyme file. Run REBASEEXTRACT

I believe this program should use a data file for restriction enzymes, Rebase. I noticed this is missing from our installation under ~/data/REBASE subdir. I just see a "dummyfile" there.

I have a few questions on EMBOSS restriction analysis and will appreciate any ideas or thoughts on these.

1. What Rebase file we need to download to get "restrict" working? I tried but there are files with different formats.
2. Is there a maximum size limit of a nucleotide sequence that I can use? Can I use the whole Human genome or at least a full chromosome to digest with a particular restriction enzyme?
3. What program can give me the list of all possible fragments generated as well? Since I have not seen the output of "restrict", perhaps that is already doing that.

Thanks for any suggestions.
Perdeep Mehta

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