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