storing long strings (DNA sequence) in R

Question

I have written a function that finds the indices of subsequences in a long DNA sequence. It works when my longer DNA sequence is < about 4000 characters. However, when I

Answer 1

Rather than write your own function, why not use the function words.pos in package seqinr. It seems to work even for strings up to a million base pairs.

For example,

library(seqinr)
data(ec999)
myseq <- paste(ec999[[1]], collapse="")
myseq <- paste(rep(myseq,100), collapse="")
words.pos("atat", myseq)