**10**wrote:

Hi!

I am trying to compare 100 peptide sequences to each other using the default settings of twoSeqSim and parSeqSim from the protr package (local alignment and BLOSUM62 substitution matrix). However, the results are different using the two functions. Using my CompareAll function, which executes twoSeqSim multiple times to compare all peptides in a vector, I've got integer scores in the similarity matrix. However, when I run parSeqSim on the same peptide set, it seems that it somehow normalizes the result values, since the results are between 0 and 1. How does this normalization work? Thanks!

```
# twoSeqSim
CompareAll <- function(eps) { # does pairwise comparisions for every peptides in the vector
simmtx <- matrix(nrow = length(pep),
ncol = length(pep),
dimnames = list(pep, pep))
for (i in 1:length(pep)) {
for (j in i:length(pep)) {
simmtx[i, j] <- twoSeqSim(pep[i], pep[j])@score
}
}
return(simmtx)
}
# parSeqSim
parSeqSim(peptides_tmp)
```

**31k**• written 2.2 years ago by lefthandgergo •

**10**