++++++++++++++++++++++++++++++++++++++++ Align: polite, proper sequence alignment ++++++++++++++++++++++++++++++++++++++++

:Authors: Marcin Cieślik, Brent Pedersen (brentp), Wibowo Arindrarto (bow)
:Email: (marcin), [email protected], [email protected]
:License: BSD

.. contents ::

About

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

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-------------------