skbio.alignment.local_pairwise_align_ssw

skbio.alignment.local_pairwise_align_ssw()

Align query and target sequences with Striped Smith-Waterman.

Parameters:

sequence1 : str or BiologicalSequence

The first unaligned sequence

sequence2 : str or BiologicalSequence

The second unaligned sequence

Returns:

skbio.alignment.Alignment

The resulting alignment as an Alignment object

Notes

This is a wrapper for the SSW package [R115].

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 and zero_index

If an alignment does not meet a provided filter, None will be returned.

References

[R115](1, 2) 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