The biomanycores biojava library.
=================================
http://www.biomanycores.org



The package provides an interface between biojava objects and
biomanycores tools.


How to install ?
----------------

You need ant and java 1.6 to run and compile the API.

The biojava API is included into the distribution as well as the
Trilead SSH for Java (see trileadsshLicence.txt).

You have to install the CUDA programs (PadovaSW, BielefeldPknotsRG and
LillePWM) before running biomanycores (see www.biomanycores.org).

Once the programs have been installed, you have to edit the config.xml
file in order to set paths and program names accordingly to your
installation.

Then you can use the biomanycores API and/or run demo programs. The
documentation of the API can be produced using 'ant doc'.



Demo programs
-------------

We can run demo programs (source code in the src/test directory and
data in the test directory). GPU mode and CPU mode are available for
each program. That is the program is launched using the GPU card or
not.

Each command line must be launched from the biomanycores directory.

* PadovaSW: Smith-Waterman alignment of protein sequences
ant testsw        : a protein sequence against another protein sequences, GPU mode
ant testswbank    : a protein sequence against a set of protein sequences, GPU mode
ant testswcpu     : CPU mode
ant testswbankcpu : CPU mode

* BielefeldPknotsRG: compute pseudonots for a RNA sequence
ant testpknots    : GPU mode
ant testpknotscpu : CPU mode

* LillePWM: scan a position frequency matrix against a DNA sequence
ant testpwm    : GPU mode
ant testpwmcpu : CPU mode