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.
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
.
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.
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