nwalign {dada2} | R Documentation |
Needleman-Wunsch alignment.
Description
This function performs a Needleman-Wunsch alignment between two sequences.
Usage
nwalign(
s1,
s2,
match = getDadaOpt("MATCH"),
mismatch = getDadaOpt("MISMATCH"),
gap = getDadaOpt("GAP_PENALTY"),
homo_gap = NULL,
band = -1,
endsfree = TRUE,
vec = FALSE
)
Arguments
s1 |
(Required). character(1) . The first sequence to align. A/C/G/T only.
|
s2 |
(Required). character(1) . The second sequence to align. A/C/G/T only.
|
match |
(Optional). numeric(1) . Default is getDadaOpt("MATCH").
The score of a match in the alignment.
|
mismatch |
(Optional). numeric(1) . Default is getDadaOpt("MISMATCH").
The score of a mismatch in the alignment.
|
gap |
(Optional). numeric(1) . Default is getDadaOpt("GAP_PENALTY").
The alignment gap penalty. Should be negative.
|
homo_gap |
(Optional). numeric(1) . Default NULL (no special homopolymer penalty).
The alignment gap penalty within homopolymer regions. Should be negative.
|
band |
(Optional). numeric(1) . Default -1 (no banding).
The Needleman-Wunsch alignment can be banded. This value specifies the radius of that band.
Set band = -1 to turn off banding.
|
endsfree |
(Optional). logical(1) . Default TRUE.
Allow unpenalized gaps at the ends of the alignment.
|
vec |
(Optional). logical(1) . Default FALSE.
Use DADA2's vectorized aligner instead of standard DP matrix. Not intended for long sequences (>1kb).
|
Value
character(2)
. The aligned sequences.
Examples
sq1 <- "CTAATACATGCAAGTCGAGCGAGTCTGCCTTGAAGATCGGAGTGCTTGCACTCTGTGAAACAAGATA"
sq2 <- "TTAACACATGCAAGTCGAACGGAAAGGCCAGTGCTTGCACTGGTACTCGAGTGGCGAACGGGTGAGT"
nwalign(sq1, sq2)
nwalign(sq1, sq2, band=16)
[Package
dada2 version 1.18.0
Index]