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

Parameters:

seq1 : str or BiologicalSequence

The first unaligned sequence.

seq2 : str or BiologicalSequence

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:

skbio.Alignment

Alignment object containing the aligned sequences as well as details about the alignment.

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.