[EMBOSS] cirdna

Jon Ison jison at ebi.ac.uk
Fri Dec 9 18:15:15 UTC 2005

Hi Ryan

The request is now logged which means that we'll certainly take a
look at doing something for the next release.  If your users have
specific requirements or specification for such a program, if you
forward them, they could be incorporated into any eventual design.



> 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?
> Ryan
> -----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
> this.
> Still, if there is enough demands from our users we can do it ....
> regards,
> Peter
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