Biomanycores biopython interfaces
=================================
http://www.biomanycores.org


This package provides an interface between some many-core applications and biopython objects.
The source code is made available under the Biopython License.

Requires Biopython >= 1.50b

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

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

Once the programs have been installed, you have to edit the Biomanycores/__init__.py
file in order to set paths and program names accordingly to your
installation, and run "python setup.py install"

Then you can use the biomanycores API and/or run demo programs. 


Demo program
------------

python demo.py cpu  (CPU mode)
python demo.py gpu  (GPU mode)

* PadovaSW: Smith-Waterman alignment of protein sequences
* BielefeldPknotsRG: compute pseudonots for a RNA sequence
* LillePWM: scan a position frequency matrix against a DNA sequence