skbio.alignment.local_pairwise_align_ssw¶
- skbio.alignment.local_pairwise_align_ssw(sequence1, sequence2, **kwargs)[source]¶
Align query and target sequences with Striped Smith-Waterman.
Note
Deprecated as of 0.5.8 for removal in 0.6.0. This will be removed or replaced, in favor of more general-purpose performant aligners. Additional details at https://github.com/biocore/scikit-bio/issues/1814
- Parameters
- Returns
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.- Return type
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
See also