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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