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:
  • sequence1 (DNA, RNA, or Protein) – The first unaligned sequence

  • sequence2 (DNA, RNA, or Protein) – The second unaligned sequence

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:

tuple

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