skbio.alignment.local_pairwise_align_ssw(sequence1, sequence2, **kwargs)[source]#

Align query and target sequences with Striped Smith-Waterman.

sequence1DNA, RNA, or Protein

The first unaligned sequence

sequence2DNA, RNA, or Protein

The second unaligned sequence


Additional keyword arguments to pass to StripedSmithWaterman.


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.


local_pairwise_align_ssw is deprecated as of 0.5.8 and will be removed in favor of more general-purpose and performant aligners. Additional details at scikit-bio/scikit-bio#1814.


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.



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.