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Notes on application for codon usage / composition bias

 Subject: Re: [EMBOSS] cirdna
From: "Ryan Golhar" 
Date: Thu, December 8, 2005 3:30 pm
To: emboss@emboss.open-bio.org
Priority: Normal
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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@ebi.ac.uk [mailto:pmr@ebi.ac.uk]
Sent: Thursday, December 08, 2005 4:28 AM
To: emboss@emboss.open-bio.org
Cc: golharam@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

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 ....



Date: 2006-02-06 14:14
Sender: jonsourceforge
Logged In: YES 

COULD ALSO LOOK AT "utopia" - Jon Ison

Date: 2005-12-12 11:02
Sender: nobody
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Subject:   	[emboss-bug] tacg
From:   	ajb@ebi.ac.uk
Date:   	Mon, December 12, 2005 10:50 am
To:   	emboss-bug@emboss.open-bio.org
Priority:   	Normal
Options:   	View Full Header |  View Printable Version


I remember looking at this in the past. Just had another
quick look. Although
GPL licenced 'twould be best done as EMBASSY if at all.
be a fair amount
of work (e.g. it uses GCG pattern/REBASE files).

It also doesn't compile using gcc 4.02 - but that's
just 4
changes. The code
still looks horrible. It won't work properly as-is on
without a bit of


Date: 2005-12-12 09:58
Sender: jonsourceforge
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Subject:   	RE: [EMBOSS] cirdna
From:   	"Ryan Golhar" 
Date:   	Fri, December 9, 2005 6:24 pm
To:   	"'Jon Ison'" 
Cc:   	emboss@emboss.open-bio.org
Priority:   	Normal
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Hi Jon,

Thanks.  Sure, I'll keep you informed.  Right now, I'm
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


-----Original Message-----
From: Jon Ison [mailto:jison@ebi.ac.uk] 
Sent: Friday, December 09, 2005 1:15 PM
To: golharam@umdnj.edu
Cc: emboss@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
requirements or specification for such a program, if you
forward them,
they could be incorporated into any eventual design.