[EMBOSS] cirdna

Ryan Golhar golharam at umdnj.edu
Fri Dec 9 18:24:24 UTC 2005

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.


-----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.



> 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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