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.
seq1 (Protein) – The first unaligned sequence.
seq2 (Protein) – 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).
substitution_matrix (2D dict (or similar), optional) – Lookup for substitution scores (these values are added to the previous best alignment score); default is BLOSUM 50.
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_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 1.
The BLOSUM (blocks substitution matrices) amino acid substitution matrices were originally defined in 2.
References