[EMBOSS] cirdna

[David.Bauer at SCHERING.DE]

What about replacing cirdna with tacg ?

http://tacg.sourceforge.net/

Cheers,
David.
emboss-bounces at emboss.open-bio.org schrieb am 09/12/2005 19:24:24:

> Hi Jon,
>
> Thanks.  Sure, I'll keep you informed.  Right now, I'm only aware of
> users wanting to be able to map restriction sites in a circular piece of
> DNA by just inputting their DNA sequence and getting the output from
> cirdna.  If I get anything more specific, I'll let you know.
>
> Ryan
>
>
> -----Original Message-----
> From: Jon Ison [mailto:jison at ebi.ac.uk]
> Sent: Friday, December 09, 2005 1:15 PM
> To: golharam at umdnj.edu
> Cc: emboss at emboss.open-bio.org
> Subject: Re: [EMBOSS] cirdna
>
>
> 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.
>
> Cheers
>
> Jon
>
>
>
> > 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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> > EMBOSS at emboss.open-bio.org
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> >
>
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