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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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nwalign-0.2.tar.gz (43.6 kB view hashes)

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