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: | seq1 : DNA, RNA, or TabularMSA[DNA|RNA]
seq2 : DNA, RNA, or TabularMSA[DNA|RNA]
gap_open_penalty : int or float, optional
gap_extend_penalty : int or float, optional
match_score : int or float, optional
mismatch_score : int or float, optional
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
, 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 [R207207].
This function can be use to align either a pair of sequences, a pair of alignments, or a sequence and an alignment.
References
[R207207] | (1, 2) http://blast.ncbi.nlm.nih.gov/Blast.cgi |