[Biopython-dev] Re: [BioPython] Tool for Biomolecular data edition and analysis in Python

Iddo Friedberg idoerg at burnham.org
Sun May 29 02:13:37 EDT 2005


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 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
Automated Protein Function Prediction Meeting, June 24, 2005

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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