[GSoC] Fwd: [Biojava-dev] Work completed for GSoC:AAPropertiesComputation

[Peter Troshin]

-------- Original Message --------
Subject: 	[Biojava-dev] Work completed for GSoC:AAPropertiesComputation
Date: 	Thu, 25 Aug 2011 10:12:43 +0800
From: 	Chuan Hock Koh <kohchuanhock at gmail.com>
To: 	biojava-l at lists.open-bio.org, biojava-dev 
<biojava-dev at lists.open-bio.org>



Hi All,

The Google Summer of Code has come to an end. Please allow me to share with
you what was achieved during this summer by me, Andreas Prlic and Peter
Troshin.

1) A set of APIs to compute Physico-Chemical properties of protein
sequences. Please see CookBook (
http://biojava.org/wiki/BioJava:CookBook:AAPROP:main) on how to use them.
Following is a list of properties that could be generated:

    - Molecular weight
    - Extinction coefficient
    - Instability index
    - Aliphatic index
    - Grand Average of Hydropathy
    - Isoelectric point
    - Amino acid composition


2) A executable jar to do the same thing as point 1. Please see CookBook (
http://biojava.org/wiki/BioJava:CookBook:AAPROP:commandprompt) for examples
on usage.

3) A set of APIs to compute PROFEAT properties of protein sequences. Please
see this paper (
http://nar.oxfordjournals.org/content/34/suppl_2/W32.abstract) for more
details about PROFEAT properties. Also, do see CookBook (
http://biojava.org/wiki/BioJava:CookBook:AAPROP:profeat) on how to use them.

4) Another thing worth noting is that as requested by the BioJava community,
we have enabled the customization for the computing of molecular weight for
point 1 and 2. Please see CookBook (
http://biojava.org/wiki/BioJava:CookBook:AAPROP:xmlfiles) for more
information.

5) Also, a SOAP web service for physico-chemical properties computation
(point 1) was developed within the JABAWS framework for portable web
services (http://www.compbio.dundee.ac.uk/jabaws/). This web service can be
installed on your own computing infrastructure with ease. If you intend to
use this web service, please contact us for further details.

I would continue to improve and work on this package even after this summer.
Therefore, if you have any feedback or comments. Please feel free to drop me
a mail. Thanks!

Regards,
Chuan Hock Koh (aka Ah Fu), Andreas Prlic and Peter Troshin

-- 
http://compbio.ddns.comp.nus.edu.sg/~ChuanHockKoh<http://compbio.ddns.comp.nus.edu.sg/~ChuanHockKoh/index.html>
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