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# skbio.alignment.local_pairwise_align_nucleotide

`skbio.alignment.``local_pairwise_align_nucleotide`(seq1, seq2, gap_open_penalty=5, gap_extend_penalty=2, match_score=2, mismatch_score=-3, substitution_matrix=None)

  Locally align exactly two nucleotide seqs with Smith-Waterman

  State: Experimental as of 0.4.0.

  Parameters:

  - seq1 (DNA or RNA) – The first unaligned sequence.
  - seq2 (DNA or RNA) – The second unaligned sequence.
  - gap_open_penalty (int or float, optional) – Penalty for opening a gap (this is substracted from previous best alignment score, so is typically positive).
  - gap_extend_penalty (int or float, optional) – Penalty for extending a gap (this is substracted from previous best alignment score, so is typically positive).
  - match_score (int or float, optional) – The score to add for a match between a pair of bases (this is added to the previous best alignment score, so is typically positive).
  - mismatch_score (int or float, optional) – The score to add for a mismatch between a pair of bases (this is added to the previous best alignment score, so is typically negative).
  - substitution_matrix (2D dict (or similar)) – Lookup for substitution scores (these values are added to the previous best alignment score). If provided, this overrides `match_score` and `mismatch_score`.

  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

  See also

  `local_pairwise_align()`, `local_pairwise_align_protein()`, `skbio.alignment.local_pairwise_align_ssw()`, `global_pairwise_align()`, `global_pairwise_align_protein()`, `global_pairwise_align_nucelotide()`

  Notes

  Default `match_score`, `mismatch_score`, `gap_open_penalty` and `gap_extend_penalty` parameters are derived from the NCBI BLAST Server [1].

  References

  [1] | http://blast.ncbi.nlm.nih.gov/Blast.cgi