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

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.

Notes

Default match_score, mismatch_score, gap_open_penalty and gap_extend_penalty parameters are derived from the NCBI BLAST Server [R108].

References

[R108](1, 2) http://blast.ncbi.nlm.nih.gov/Blast.cgi