[EMBOSS] Antwort: restrict

[david.bauer at bayerhealthcare.com]

Hi,

emboss-bounces at lists.open-bio.org schrieb am 23/02/2010 00:21:38:

> 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.

Go to the /pub/rebase dir on ftp.neb.com.
Download the withrefm.xxx and proto.xxx files
(xxx stands for the version number, just take the latest that's there)
Run rebaseextract -infile withrefm.xxx -protofile proto.xxx
This reformats the neb files for use with emboss. You should now see 
4 files embossre.... in the REBASE directory

> 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?

I'm not sure about the whole genome but I have used it for individual
chromosomes without problems.

> 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.

You can run restrict with the option -fragments to get them.

Hope this helps,
David.