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)[source]#

Locally align exactly two nucleotide seqs with Smith-Waterman.

Parameters:

seq1DNA or RNA: The first unaligned sequence.
seq2DNA or RNA: The second unaligned sequence.
gap_open_penaltyint or float, optional: Penalty for opening a gap (this is substracted from previous best alignment score, so is typically positive).
gap_extend_penaltyint or float, optional: Penalty for extending a gap (this is substracted from previous best alignment score, so is typically positive).
match_scoreint 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_scoreint 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.