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.
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.
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_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