skbio.alignment.global_pairwise_align_protein

skbio.alignment.global_pairwise_align_protein(seq1, seq2, gap_open_penalty=11, gap_extend_penalty=1, substitution_matrix=None, penalize_terminal_gaps=False)[source]

Globally align pair of protein seqs or alignments with Needleman-Wunsch

State: Experimental as of 0.4.0.

Parameters

  • seq1 (Protein or TabularMSA[Protein]) – The first unaligned sequence(s).

  • seq2 (Protein or TabularMSA[Protein]) – The second unaligned sequence(s).

  • 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.

  • penalize_terminal_gaps (bool, optional) – If True, will continue to penalize gaps even after one sequence has been aligned through its end. This behavior is true Needleman-Wunsch alignment, but results in (biologically irrelevant) artifacts when the sequences being aligned are of different length. This is False by default, which is very likely to be the behavior you want in all or nearly all cases.

Returns

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.

Return type

tuple

See also

local_pairwise_align(), local_pairwise_align_protein(), local_pairwise_align_nucleotide(), skbio.alignment.local_pairwise_align_ssw(), global_pairwise_align(), 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.

This function can be use to align either a pair of sequences, a pair of alignments, or a sequence and an alignment.

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.