[Biojava-l] GSoC project on MSA

[Andreas Prlic]

Hi Gustavo,

With straightforward I meant that we only have 3 months for this project and
we should not try to solve all problems at the same time. Probably a
realistic approach is to start with trying to keep things modular and simple
(think interfaces and implementations) and stick to standard solutions that
have been shown to work elsewhere. If there is more time in the project one
can then replace some of the implementations with technically more advanced
ones.

Since we are doing things in Java I am interested in having support for
parallelisation wherever possible. Another issue is how to verify that the
created alignments are meaningful. One could e.g. use the biojava structure
modules to calculate protein structure alignments to verify the quality of
the obtained multiple sequence alignments.

All applications have to be made via Google. We are providing comments  on
drafts of proposals and try to work together with applicants to improve the
submissions. Note: The application deadline is soon and speed is important
now.

Andreas



On Mon, Apr 5, 2010 at 10:29 PM, Gustavo Akio Tominaga Sacomoto <
sacomoto at gmail.com> wrote:

> Hello,
>
> I'm currently a graduate student at University of São Paulo (Brazil)
> and I'm quite interested in applying for the all-Java MSA project. I'm
> already familiar with the multiple sequence alignment problem, I
> developed a lossless filter for this problem as my undergraduate final
> project, the work is described here
> [http://www.almob.org/content/4/1/3] and there is an online version of
> the algorithm here
> [http://mobyle.genouest.org/cgi-bin/Mobyle/portal.py?form=tuiuiu].
>
> Now, regarding the project, just to make it clear, when you say in the
> "straightforward approach for building up the MSA progressively", you
> mean the standard dynamic programming approach for pairwise alignment
> following the guide tree built in the second step, right?
>
> One last question, should I send my proposal direct to the Google's
> web app or here first?
>
> Thanks,
>
> Gustavo Sacomoto
>
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-- 
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Dr. Andreas Prlic
Senior Scientist, RCSB PDB Protein Data Bank
University of California, San Diego
(+1) 858.246.0526
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