skbio.alignment.
local_pairwise_align_protein
(seq1, seq2, gap_open_penalty=11, gap_extend_penalty=1, substitution_matrix=None)[source]¶Locally align exactly two protein seqs with Smith-Waterman
State: Experimental as of 0.4.0.
Parameters: | seq1 : Protein
seq2 : Protein
gap_open_penalty : int or float, optional
gap_extend_penalty : int or float, optional
substitution_matrix: 2D dict (or similar), optional
|
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Returns: | tuple
|
See also
local_pairwise_align
, local_pairwise_align_nucleotide
, skbio.alignment.local_pairwise_align_ssw
, global_pairwise_align
, global_pairwise_align_protein
, global_pairwise_align_nucelotide
Notes
Default gap_open_penalty
and gap_extend_penalty
parameters are
derived from the NCBI BLAST Server [R105].
The BLOSUM (blocks substitution matrices) amino acid substitution matrices were originally defined in [R106].
References
[R105] | (1, 2) http://blast.ncbi.nlm.nih.gov/Blast.cgi |
[R106] | (1, 2) Amino acid substitution matrices from protein blocks. S Henikoff and J G Henikoff. Proc Natl Acad Sci U S A. Nov 15, 1992; 89(22): 10915-10919. |