[BioPython] Tool for Biomolecular data edition and analysis in Python

[Iddo Friedberg]

Frederico,

This looks like a really useful tool, thanks for sharing.

One way I can see this fitting into Biopython is as an addition to the
Align module. We'll have to think exactly how.

However, I am wondering if this really fits within biopython: you have
what seems to me as a standalone program. Biopython's goal is to provide
buiding blocks for such tools. So your code is the next step: you have
constructed a house (a very fine one, may I add), Biopython provides
lumber, bricks, etc. etc.

Like I said, I'll have to look at it. But with ISMB coming up, it will
probably not be for a month. If someone else has any thoughts on the
matter, please share.

Cheers, and thanks again,

Iddo




--
Iddo Friedberg, Ph.D.
The Burnham Institute
10901 N. Torrey Pines Rd.
La Jolla, CA 92037, USA
Tel: +1 (858) 646 3100 x3516
Fax: +1 (858) 646 3171
http://ffas.ljcrf.edu/~iddo
-------------------------------------
Automated Protein Function Prediction Meeting, June 24, 2005
http://ffas.burnham.org/AFP

On Sat, 28 May 2005, Frederico Arnoldi wrote:


> Hello,
> 
>    My name is Frederico G. Colombo Arnoldi, I am Phd student (subject:
> Molecular Evolution) in Brazil.
>   I have been developing a software for Biomolecular data edition and
> analysis in python, mainly for gene analysis. It started as a little
> tool to help me and became a more serious work. Actually this tool is
> formed by a GTK interface that allows the user to align sequences with
> Malign and Clustalw; color sequences previously aligned according
> conservation and residues characteristics; create reverse,
> reverse/complement and consensus sequences; search for conserved
> regions and determined sequences inside a bigger (like restriction
> enzymes sites and ORF's); generate alignments colored reports and
> others.
>    The program and Its portal has been written in English, although,
> as anyone can see in my bad english, I'm not a native english speaker.
>     I would like to know about the possibility and the interest of
> integrate it to biopython. The portal is : 
> http://mpalign.incubadora.fapesp.br/portal
> 



>     Thanks a lot.
>     Frederico
> 
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