[EMBOSS] suggestion for improving restrict - Checked by AntiVir DEMO version -

[Guy Bottu]

        Dear users and developers of EMBOSS,

One of our users has a suggestion for improvinf restrict. He needs a list
with the lengths of the restriction fragments, in the same order as they
appear on the plasmid.
Do you think this is an intersting addition ? (Note also how I suggested
him to get around using Excel).

        Regards,
        Guy Bottu,
        BEN

----- Forwarded message from Xavier Danthinne <xdanthin at od260.com> -----

From: "Xavier Danthinne" <xdanthin at od260.com>
To: "BEN administration" <embadmin at ben.vub.ac.be>
Subject: Re: EMBOSS - Checked by AntiVir DEMO version - - Checked by 
AntiVir
+DEM
Date: Fri, 8 Jun 2007 10:16:10 -0600
X-Priority: 3
X-MSMail-Priority: Normal
X-Mailer: Microsoft Outlook Express 6.00.2900.3028
X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2900.3028
X-Authentication-Info: Submitted using SMTP AUTH LOGIN at
+imta07a2.registeredsite.com from [63.79.129.51] using ID 
xdanthin at od260.com at
+Fri, 8 Jun 2007 12:16:02 -0400
X-AntiVirus: checked by AntiVir Milter 1.0.6; AVE 7.4.0.32; VDF 6.38.2.8

Hello Guy,
I read the exercise #6 that you mentioned, and the third paragraph ("Now
suppose that...") is exactly what I was looking for.  I understand that the
solution is to save the data from "restrict" as tab-delimited, so we can
import them into excel and calculate in a new column the difference between
one site and the next one.  This is not such a big deal to do that each
time, but if the program restrict could do it for us, that would be great.
This is what computers are for, isn't it?
Thanks for your help, and have a good weekend.
Xavier

Xavier Danthinne, Ph.D.
O.D.260 Inc
PO Box 534
Boise, ID 83701

Ph. (208)345-7369
Fax (208)345-7569
Cell (208)484-0104
----- Original Message -----

From: "BEN administration" <embadmin at ben.vub.ac.be>
To: "Xavier Danthinne" <xdanthin at od260.com>
Sent: Friday, June 08, 2007 3:25 AM
Subject: Re: EMBOSS - Checked by AntiVir DEMO version -


>On Wed, Jun 06, 2007 at 11:52:21PM -0600, Xavier Danthinne wrote:
>>I still like using EMBOSS.  I have a suggestion regarding the program
>>"restrict".  If the program could list restriction fragments with their
>>size in the order by which they constitute a piece of DNA such as a
>>plasmid, this would be great.  I work with large cosmids, and it is
>>sometimes difficult to figure out where a specific fragment is located
>>among others.  Having this feature (like we had in GCG) would help.
>
>Well, you can export the output in MS Excel format and then quite easily
>comute the list you want. The exercise 6 from
>ftp://ftp.be.embnet.org/pub/BEN_Tutorials/unix_perl/ex-UNIX.doc
>gives you an example of how to.
>If you use wEMBOSS rather then the command line the parameters to set are
>"Comma separated enzyme list" ...  "Allow circular DNA?" y "Sort output
>alphabetically?" y (or n, dependant on your needs) "Report format"
>tab-delimited table format.
>Does this help ?
>
>Regards,
>Guy Bottu
>

----- End forwarded message -----