nw.sat.quer: Needleman-Wunsch for many sequenes.

In needleman.wunsch: Needleman Wunsch computation

Description

Few/many to many pairwise comparisons with two sets of sequences (satellites and queries)

Usage

nw.sat.quer(satellites, queries, S, g)
nws.sat.quer(satellites, queries, S, g)
qnw.sat.quer(satellites, queries)

Arguments

satellites	satellite sequences (list of integer vectors).
queries	other sequences (list of integer vectors).
S	a scoring matrix (nw.sat.quer) reshaped as vector or a short vector (nws.sat.quer) 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

satellites <- char2int(c("ACGT", "ACGG"))
queries    <- char2int(c("ACGT", "ACGGG"))
nw.sat.quer(satellites, queries, c(1,-1,-1,-1,-1,1,-1,-1,-1,-1,1,-1,-1,-1,-1,1), -1)
nws.sat.quer(satellites, queries, c(1,-1), -1)
qnw.sat.quer(satellites, queries)

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