Skip to main content
`Ctrl`+`K`

# 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.

  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:
    tuple

      `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.

  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