Needleman-Wunsch global sequence alignment
Project description
This module provides a python module and a command-line interface to do global- sequence alignment using the Needleman-Wunsch algorithm. It uses cython and numpy for speed.
Example Command-Line Usage
the nwalign executable is installed to the PATH by setuptools:
$ nwalign alphabet alpet alphabet alp---et
specify an alignment scoring matrix
$ nwalign --matrix /usr/share/ncbi/data/BLOSUM62 EEAEE EEEEG EEAEE- EE-EEG
Usage as a python module
>>> import nwalign as nw
>>> nw.global_align("CEELECANTH", "PELICAN", matrix='PAM250')
('CEELECANTH', '-PELICA--N')
the matrix is specified as the full path to an scoring matrix as is distributed with the NCBI toolset.
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