- Authors
Marcin Cieślik, Brent Pedersen (brentp), Wibowo Arindrarto (bow)
(marcin), bpederse@gmail.com, bow@bow.web.id
- License
BSD
Various packages implement sequence alignment algorithms with various levels of success. This package is an attempt to handle the sequence alignment properly, including edge-cases.
usage will change. currently :
>>> from align.matrix import DNAFULL
>>> from align import aligner
>>> aligner('WW','WEW', method= 'global')
('W-W', 'WEW')
>>> aligner('WW','WEWWEW', method= 'glocal')
('WW', 'WW')
>>> aligner('TAATTC', 'TAAT', method='global', matrix=DNAFULL, gap_open=-10, gap_extend=-1)
('TAATTC', 'TAAT--')
>>> aligner('PYNCHAN', 'YNCH', method='local')
('YNCH', 'YNCH')
>>> a, b = aligner('AAAAAAAAAAAAACCTGCGCCCCAAAAAAAAAAAAAAAAAAAA', 'CCTGCGCACCCC', method='global_cfe')
>>> print "%s\n%s" % (a, b)
AAAAAAAAAAAAACCTGCGC-CCCAAAAAAAAAAAAAAAAAAAA
-------------CCTGCGCACCCC-------------------