Locally align exactly two protein seqs with Smith-Waterman
Parameters: | seq1 : str or BiologicalSequence
seq2 : str or BiologicalSequence
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: | skbio.Alignment
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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 [R113].
The BLOSUM (blocks substitution matrices) amino acid substitution matrices were originally defined in [R114].
References
[R113] | (1, 2) http://blast.ncbi.nlm.nih.gov/Blast.cgi |
[R114] | (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. |