skbio.alignment.
local_pairwise_align_ssw
(sequence1, sequence2, **kwargs)[source]¶Align query and target sequences with Striped Smith-Waterman.
State: Experimental as of 0.4.0.
TabularMSA
object containing the aligned sequences, alignment score
(float), and start/end positions of each input sequence (iterable
of two-item tuples). Note that start/end positions are indexes into the
unaligned sequences.
tuple
Notes
This is a wrapper for the SSW package 1.
For a complete list of optional keyword-arguments that can be provided,
see skbio.alignment.StripedSmithWaterman
.
The following kwargs will not have any effect: suppress_sequences, zero_index, and protein
If an alignment does not meet a provided filter, None will be returned.
References
Zhao, Mengyao, Wan-Ping Lee, Erik P. Garrison, & Gabor T. Marth. “SSW Library: An SIMD Smith-Waterman C/C++ Library for Applications”. PLOS ONE (2013). Web. 11 July 2014. http://www.plosone.org/article/info:doi/10.1371/journal.pone.0082138