skbio.alignment.local_pairwise_align_protein

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

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.

Returns:

tuple

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.

Notes

Default gap_open_penalty and gap_extend_penalty parameters are derived from the NCBI BLAST Server [R109].

The BLOSUM (blocks substitution matrices) amino acid substitution matrices were originally defined in [R110].

References

[R109](1, 2) http://blast.ncbi.nlm.nih.gov/Blast.cgi
[R110](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.