From antoniov@cc.hut.fi Tue Nov 21 14:03:45 2000
Date: Mon, 20 Nov 2000 11:43:05 +0200
From: Antonio Villena Borrego <antoniov@cc.hut.fi>
To: janne.nikkila@hut.fi
Subject: Project Work for BioInformatics

Hello Janne,

    I'm a student of BioInformatics (Tik-61.181). My name is Antonio Villena
Borrego with student number 55809H. I was thinking about the small research
project which is needed to be done in order to pass the course, and I've
just thought of doing the following:

    I'm planning to implement one of the alignment algorithms explained in
chapter 2 of the book: "Biological Sequence Analysis" by R. Dubin, S. Eddy,
A. Krogh and G. Mitchison. The one I've choosed is the Neddleman-Wunsch
algorithm for obtaining optimal alignment between two different sequences of
amino-acids, allowing gaps. As for the scoring system I'll be using the
BLOSUM50 table detailed in the same book which is based on log-odds scoring
system.

    I'll be programing the algorithm using C lenguage compiled under a
Windows platform. Because it's for academic purpose, I don't think it's
neccesary to develop a graphical user interface for the program, so I'll be
doing it using a text-based interface, just like MS-DOS.

    I think this is the intended amount of work designed for the research
project. But if you consider this to be few or too much work compared to
what you have in mind please tell me and we will see how we can arranged it.

    Please reply as soon as possible,

With Best Regards,
Antonio Villena Borrego