[EMBOSS] sixpack

[Derek Gatherer]

Hi Jon et al

First of all congrats on the new EMBOSS funding.

Stefan has pointed to an important problem - we really need a good 
_flexible_ translator.  The current bunch are powerful and fast but 
too rigid and in some cases don't appear to do what they say on the 
tin.  See my previous posts:

http://emboss.open-bio.org/pipermail/emboss/2006-February/002433.html
http://emboss.open-bio.org/pipermail/emboss/2006-February/002434.html

I have also some private correspondence with Alan, and Gary Williams, 
about these issues which I'd be happy to forward with their 
permission.  What we need is an app that enables you to say: take 
this sequence or sequences, translate them from various x to various 
y, specifying strand, and give me output format z.  Currently we 
don't quite have that.  If you could tweak the existing 
showseq/prettyseq/sixpack, it would be great.

Cheers
Derek

At 15:49 04/05/2006, you wrote:
>Hi Stefan
>
>The short answer is no, but both would be easy to easy to
>implement as ACD options - perhaps for the next release.
>Please send an example of the fasta description line you
>have in mind.
>
>Cheers
>
>Jon
>
>
>
> > Dear all,
> >
> > is there a way to create a sixpack output that contains the n.a. ORFs
> > and/or their coordinates in the fasta description line?
> >
> > Also, is there an option to output the longest ORF only?
> >
> > And yes, both would be useful. ;)
> >
> > Cheers, Stefan
> >
> >
> > --
> > Dr. Stefan Rensing, Group Leader Computational Biology
> > Plant Biotechnology, Faculty of Biology, University of Freiburg
> > Schaenzlestr. 1, D-79104 Freiburg, Fon: +49 761 203-6974, Fax: -6945
> > http://www.plant-biotech.net/ http://www.cosmoss.org/
> > stefan.rensing at biologie.uni-freiburg.de
> >
> > "I want you to take him from his hotel, drug him, put him in the
> >  front of a car, and run a truck into it at 50 mph."
> > _______________________________________________
> > EMBOSS mailing list
> > EMBOSS at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/emboss
> >
>
>
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