skbio.alignment.
global_pairwise_align
(seq1, seq2, gap_open_penalty, gap_extend_penalty, substitution_matrix, penalize_terminal_gaps=False)[source]¶Globally align a pair of seqs or alignments with Needleman-Wunsch
State: Experimental as of 0.4.0.
Parameters: | seq1 : GrammaredSequence or TabularMSA
seq2 : GrammaredSequence or TabularMSA
gap_open_penalty : int or float
gap_extend_penalty : int or float
substitution_matrix: 2D dict (or similar)
penalize_terminal_gaps: bool, optional
|
---|---|
Returns: | tuple
|
See also
local_pairwise_align
, local_pairwise_align_protein
, local_pairwise_align_nucleotide
, skbio.alignment.local_pairwise_align_ssw
, global_pairwise_align_protein
, global_pairwise_align_nucelotide
Notes
This algorithm (in a slightly more basic form) was originally described in [R100]. The scikit-bio implementation was validated against the EMBOSS needle web server [R101].
This function can be use to align either a pair of sequences, a pair of alignments, or a sequence and an alignment.
References
[R100] | (1, 2) A general method applicable to the search for similarities in the amino acid sequence of two proteins. Needleman SB, Wunsch CD. J Mol Biol. 1970 Mar;48(3):443-53. |
[R101] | (1, 2) http://www.ebi.ac.uk/Tools/psa/emboss_needle/ |