[Biojava-dev] [GSoC] Help!

[Nirmal Fernando]

Hi All,

As you might have seen, I have sent my draft proposal to the list few days back.

This is my second time as a Google Summer of Code student and I am
passionate for excellence.

As for the current proposal for the project "Calculation of
Physicochemical Properties of Amino Acids" [1]
I only have included the basic functionalities [2] that were asked by Peter.

But I would love to contribute more for this inspiring field, and need
the help of the community to find out
another calculation or two, regarding physicochemical properties of a
protein or a nucleotide.

I highly appreciate your valuable thoughts on this regard!

Thanks.

[1]

Project Rationale

The calculation of simple physicochemical properties for biopolymers
is an important tool in the arsenal of molecular biologist.
Theoretically calculated quantities like extinction coefficients,
isoelectric points, hydrophobicities and instability indices are
useful guides as to how a molecule behaves in an experiment. Many
tools for calculating these properties exist, including widely used
open-source implementations in EMBOSS and BioPerl, but only some are
currently available in BioJava3. The aim of this project is to port or
produce new implementations of standard algorithms for a range of
calculations within BioJava3.

[2]

Primarily focus on developing following functionalities:

   1. Finding molecular weight of a sequence
   2. Finding extinction coefficient of a protein
   3. Finding instability index of a protein
   4. Finding aliphatic index of a protein
   5. Finding GRAVY (Grand Average of Hydropathy) value of a peptide
or a protein
   6. Finding isoelectric point of a sequence
   7. Finding number of amino acids in a protein (His, Met, Cys)



--
Best Regards,
Nirmal

C.S.Nirmal J. Fernando
Department of Computer Science & Engineering,
Faculty of Engineering,
University of Moratuwa,
Sri Lanka.
Blog: http://nirmalfdo.blogspot.com/