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)

Locally align exactly two protein seqs with Smith-Waterman.

Parameters:

seq1Protein

The first unaligned sequence.

seq2Protein

The second unaligned sequence.

gap_open_penaltyint or float, optional

Penalty for opening a gap (this is substracted from previous best alignment score, so is typically positive).

gap_extend_penaltyint 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.

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

[1]

http://blast.ncbi.nlm.nih.gov/Blast.cgi

[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.