[EMBOSS] cirdna

Ryan Golhar golharam at umdnj.edu
Thu Dec 8 15:30:25 UTC 2005

We met with a group of our users and and there are quite a few who use
MapPlot from GCG to draw plasmids with restriction sites.  Migrating
from GCG to EMBOSS means we have to provide them with alternatives to
whatever tools they used in GCG.  

Someone else recommended TACG (http://tacg.sourceforge.net/).  We'd like
our users to use the web front-end (EMBOSS-Explorer by Luke McCarthy),
which means any tools must be part of EMBOSS or MYEMBOSS to be used by
EMBOSS-Explorer.  If modifying cirdna is not possible, what about
incorporating TACG as a MYEMBOSS application?


-----Original Message-----
From: pmr at ebi.ac.uk [mailto:pmr at ebi.ac.uk] 
Sent: Thursday, December 08, 2005 4:28 AM
To: emboss at emboss.open-bio.org
Cc: golharam at umdnj.edu
Subject: Re: [EMBOSS] cirdna

JOn Ison wrote:

> So far as I'm aware there are no apps to generate a cirdna input file,

> at least not directly.
> I don't think there are tools in EMBOSS to do that conversion for you 
> at the moment.  restrict can generate output as a report format
> but cirdna can't currently read a report format.   That could change
> though.  If you let us know exactly what you need we can do something 
> for a future release.

A word of caution ... I tried exactly this for cirdna and lindna a few
years ago (writing their input format as a new report format).

Unfortunately, the font sizes and layout in cirdna and lindna did not
work in many cases - for large or small sequences there was no good
standard input format that produced readable output. Every case needed
to be edited.

So, we have to also make major changes to cirdna and lindna to support

Still, if there is enough demands from our users we can do it ....



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