Authors: Marcin Cieślik, Brent Pedersen (brentp), Wibowo Arindrarto (bow) Email: (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-------------------