Hi guys,
New release sounds great! It nicely wraps up the work completed during
this year's Google Summer of Code. Thank you for making it!
Perhaps, I should say a few words about another, recently added piece of
the functionality for prediction of disordered regions from a protein
sequence.
This work is wrapped up as a /biojava3-protein-disorder/ module. For
now, this module contains one method for the prediction of disordered
regions. This method is based on the Java implementation of RONN
<http://www.strubi.ox.ac.uk/RONN> predictor.
This code has been originally developed for another project and made its
way into the BioJava.
As the main code behind this is a Java implementation of RONN,
unimaginatively we call it /JRONN/. JRONN is based on RONN version 3.1
which is still current in time of writing (August 2011) and so gives the
same predictions as RONN.
Main motivation behind JRONN development was providing an implementation
of RONN more suitable to use by the automated analysis pipelines and web
services. Robert Esnouf has kindly allowed us to explore the RONN code
and share the results with the community.
Original version of RONN is described in Yang,Z.R., Thomson,R.,
McMeil,P. and Esnouf,R.M. (2005) RONN: the bio-basis function neural
network technique applied to the detection of natively disordered
regions in proteins. Bioinformatics 21: 3369-3376
<http://bioinformatics.oxfordjournals.org/content/21/16/3369.full>
Please refer to the cookbook entry
http://biojava.org/wiki/BioJava:CookBook#biojava3-protein-disorder for
more information about disorder prediction module.
Happy coding,
Peter
P.S. I think the documentation for biojava3-protein-disorder module is
ok, unless someone can suggest any improvements.
P.P.S. Andreas, it would be great if you could remove the content of
this directory
http://www.biojava.org/download/maven/org/biojava/biojava3-protein-disorder
to get rid of outdated artefacts.
On 25/08/2011 18:06, Andreas Prlic wrote:
Hi Ah Fu and Peter,
Thank you both for your dedicated work over the summer. It is great to
see the new modules coming out of this and this further extends the
list of useful things you can use BioJava for. Let's try to make
access to these new features as easy as possible by making a new
release within the next two weeks.
I suggest to have a code freeze by Thursday September 1st (today in a
week), then I will make the release during the days after. Until then
lets make sure that the documentation is up to date and any
outstanding commits are being made.
Andreas
On Wed, Aug 24, 2011 at 7:12 PM, Chuan Hock Koh<[email protected]> wrote:
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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