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: |
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Returns: |
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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_protein()
, global_pairwise_align_nucelotide()
Notes
This algorithm (in a slightly more basic form) was originally described in [1]. The scikit-bio implementation was validated against the EMBOSS needle web server [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] | 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. |
[2] | http://www.ebi.ac.uk/Tools/psa/emboss_needle/ |