[GSoC] [gsoc]All-Java Multiple Sequence Alignment (MSA)

[Andreas Prlic]

Hi Diana,

thanks for your email. I have already been contacted by several students who
are interested in this project. As such it is not going to be easy to apply
for this project and a very well written proposal will be needed in order to
get a good ranking and to have a chance of getting selected by Google. We
are also suggesting a 2nd project for BioJava: Identification and
Classification of Posttranslational Modification of Proteins
http://biojava.org/wiki/Google_Summer_of_Code  . Besides this, Google also
invites students to propose their own ideas...

Talking about MSA, I would like to see an approach that is using modern
parallelization techniques available through Java. I don't think the goal
should be to re-implement an already existing approach but to come up with a
combination of new and already established things. There is no simple answer
to speed vs best optimum, both are important ...

Andreas


On Mon, Mar 29, 2010 at 3:18 PM, Diana Lungu <diana.irina.lungu at gmail.com>wrote:

> Hello to everyone!
>
> My name is Diana Lungu and I am an undergraduate at University Alexandru
> Ioan Cuza, Faculty of Computer Science Iasi, Romania.
>
> I am interested in Gsoc 2010 project "All-Java Multiple Sequence Alignment
> (MSA)". I have worked on several projects in Java in the last two years and
> I really enjoy Java programming. I have spent a nice amount of time
> developing with java the last two years but this will be my first open
> source project. Currently I am attending a course in Bioinformatics at my
> Faculty of Computer Science that is why I think this project suits me. There
> are several algorithms that offer an aligment from multiple sequences:
> Carrillo-Lipman, Feng and Doolittle, Barton-Stenberg etc. Is there a
> preference for one of these algorithms? What is more important: speed or the
> best optimum?
>
> Have a lovely day :)
>
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