skbio.alignment.local_pairwise_align_ssw

skbio.alignment.local_pairwise_align_ssw(sequence1, sequence2, **kwargs)

Align query and target sequences with Striped Smith-Waterman.

Parameters:

sequence1DNA, RNA, or Protein

The first unaligned sequence

sequence2DNA, RNA, or Protein

The second unaligned sequence

kwargsdict

Additional keyword arguments to pass to StripedSmithWaterman.

Returns:

tuple

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.

Warning

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.

See also

skbio.alignment.StripedSmithWaterman

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

[1]

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