[EMBOSS] Antwort: restrict

[Hotz, Hans-Rudolf]

On 2/23/10 4:04 PM, "Mehta, Perdeep" <Perdeep.Mehta at stjude.org> wrote:

> Thank you, including Duleep and David Lapointe for the prompt responses and
> for describing it in complete detail.  I got what I couldn't find going
> through REBASE website and looking into EMBOSS' web pages.  Excuse me for my
> ignorance, where can I find a manual or a good documentation on the EMBOSS
> package.

Have you looked at the EMBOSS homepage?

http://emboss.sourceforge.net/


where all the applications are nicely explained

http://emboss.sourceforge.net/apps/release/6.2/emboss/apps/groups.html


Hans

> regards,
> perdeep
> 
> 
> From: david.bauer at bayerhealthcare.com [mailto:david.bauer at bayerhealthcare.com]
> Sent: Tuesday, February 23, 2010 12:56 AM
> To: Mehta, Perdeep
> Cc: emboss; emboss-bounces at lists.open-bio.org
> Subject: Antwort: [EMBOSS] restrict
> 
> 
> 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.
> 
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