[Biojava-l] Last week of Google Summer of Code

[Andreas Prlic]

Hi,

This is the last week of this year's Google Summer of Code project and
I am happy to announce that our two students Mark Chapman and
Jianjiong Gao did an amazing job on their two projects "All Java
Multiple Sequence Alignment" (MSA) and "Identification and
Classification of Posttranslational Modification of Proteins" (PTM).

For Multiple Sequence Alignments we now have a flexible and
multi-threaded MSA implementation that works in linear space and that,
as an option, allows the users to define anchors that are used in the
build up of the multiple alignment. The code is available as part of
the new biojava3-alignment module.

The Posttranslational Modification module (biojava3-protmod) can
detect three different types of protein modifications in protein
structures. It comes with an XML file & Java data structures to store
information about different types of protein modifications, and
contains entries from RESID, PDBCC and PSI-MOD. There is also a
visualisation component to display cross linked PTM on a sequence
viewer.

Both Mark and Jianjiong have expressed their interest in maintaining
and further developing their modules and I am looking forward to
interacting more with them in the future. I want to thank the Mentors
and Co-Mentors Peter Rose, Kyle Ellrott and Scooter Willis for their
help and guidance for the projects, without them this would not have
been possible. Thanks also to Robert Buels and the  Open
Bioinformatics Foundation for organizing our applications for GSoC and
last, but not least, Google for sponsoring this Summer of Code.

Happy BioJava-ing,

Andreas