nw.sg.mult: Semi-global Needleman-Wunsch for multiple sequenes.

In needleman.wunsch: Needleman Wunsch computation

Description

Simple function using Rcpp to compute semi-global Needleman-Wunsch score. The first set of sequence are short, the second long.

Usage

nw.sg.mult(short, long, S, g)
nws.sg.mult(short, long, S, g)
qnw.sg.mult(short, long)

Arguments

short	short sequences (list of integer vectors).
long	long sequences (list of integer vectors).
S	a scoring matrix (nw.sg.mult) reshaped as vector or a short vector (nws.sg.mult) based on the scoring matrix (quicker) (see examples).
g	an integer vector holding the gap penalty.

Value

D	Matrix of scores from queries against satellites
D_scaled	Matrix of scores scaled by satellite lengths

Examples

short <- char2int(c("ACGT", "ACGG"))
long  <- char2int(c("AAACCCACGTATA", "ACGGGACGAGC"))
nw.sg.mult(short, long, matrix(c(1,-1,-1,-1,-1,1,-1,-1,-1,-1,1,-1,-1,-1,-1,1),4,4), -1)
nws.sg.mult(short, long, c(1,-1), -1)
qnw.sg.mult(short, long)

needleman.wunsch documentation built on May 2, 2019, 4:43 p.m.