Fork me on GitHub"

# 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:

  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 [R213213].

  References

  [R213213] | (1, 2) http://blast.ncbi.nlm.nih.gov/Blast.cgi