# skbio.alignment.StripedSmithWaterman¶

class skbio.alignment.StripedSmithWaterman

Performs a striped (banded) Smith Waterman Alignment.

First a StripedSmithWaterman object must be instantiated with a query sequence. The resulting object is then callable with a target sequence and may be reused on a large collection of target sequences.

Notes

This is a wrapper for the SSW package [R95].

mask_length has to be >= 15, otherwise the suboptimal alignment information will NOT be returned.

match_score is a positive integer and mismatch_score is a negative integer.

match_score and mismatch_score are only meaningful in the context of nucleotide sequences.

A substitution matrix must be provided when working with protein sequences.

References

 [R95] (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