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
seq2 : DNA or RNA
gap_open_penalty : int or float, optional
gap_extend_penalty : int or float, optional
match_score : int or float, optional
mismatch_score : int or float, optional
substitution_matrix: 2D dict (or similar)
|
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Returns: | 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 [R108].
References
[R108] | (1, 2) http://blast.ncbi.nlm.nih.gov/Blast.cgi |