rsite <- function(inseq, seq){
# inseq: vector containing input DNA sequence,
# A=1, C=2, G=3, and T=4
# seq: vector for the restriction site, length m
# Make/initialize vector to hold site
# positions found in inseq
xxx <- rep(0, length(inseq))
m <- length(seq)
#To record whether position of inseq matches seq
truth<-rep(0, m)
# Check each position to see if a site starts there.
for(i in 1:(length(inseq) - (length(seq) - 1))) {
for(j in 1:m) {
if(inseq[i + j - 1] == seq[j]) {
truth[j] <- 1 # Record match to jth position.
}
}
if(sum(truth[]) == m){# Check whether all positions match
xxx[i] <- i # Record site if all positions match
}
truth <- rep(0, m) # Reinitialize for next loop cycle
}
# Write vector of restriction site positions stored in xxx
L <- xxx[xxx > 0]
return(L)
}