Hi,

I was wondering what would be the most efficient strategy to get distances
between sequences that belong to two different sets. So far, what I am
doing is:

library(Biostrings)
set.seed(1)
alph = DNA_ALPHABET[1:4]
set1 = matrix(sample(alph, 30, rep=TRUE), nr=6)
set1 = apply(set1, 1, paste, collapse='')
set2 = matrix(sample(alph, 20, rep=TRUE), nr=4)
set2 = apply(set2, 1, paste, collapse='')
outer(set1, set2, function(x, y) apply(cbind(x, y), 1, stringDist))

Thanks a lot for any suggestion,
benilton

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