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Showing posts from April 19, 2009

Needleman-Wunsch global sequence alignment

[EDIT 01-01-2010] this is now available at bitbucket.
I've written a simple, fast, python version of Needleman-Wunsch as I couldn't find one to use. It uses Cython and specifically cython-numpy goodness. It's easy-installable as:
sudo easy_install -UZ http://bpbio.googlecode.com/svn/trunk/nwalign/
or via svn from:
svn co http://bpbio.googlecode.com/svn/trunk/nwalign/
it will put an executable 'nwalign' into /usr/bin/ which when run will give this message:

Usage:
nwalign [options] seq1 seq2


Options:
-h, --help show this help message and exit
--gap=GAP gap extend penalty (must be integer <= 0)
--gap_init=GAP_INIT gap start penalty (must be integer <= 0)
--match=MATCH match score (must be integer > 0)
--mismatch=MISMATCH gap penalty (must be integer < 0)
--matrix=MATRIX scoring matrix in ncbi/data/ format,
if not specificied, match/mismatch are used

where the matrix is optional but can be the ful…