skbio.alignment.
global_pairwise_align_nucleotide
(seq1, seq2, gap_open_penalty=5, gap_extend_penalty=2, match_score=1, mismatch_score=-2, substitution_matrix=None, penalize_terminal_gaps=False)[source]¶Globally align nucleotide 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()
, global_pairwise_align_protein()
Notes
Default match_score
, mismatch_score
, gap_open_penalty
and
gap_extend_penalty
parameters are derived from the NCBI BLAST
Server [1].
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 |