Hi dear monks!

I'm in the need of checking 2 strings for degree of identity, and right now I'm doing this by checking char by char via 'substr()':

for (my $i = 0; $i < $len; $i++) {
   $score += ((substr($ref_seq, $i, 1)) eq (substr($test_seq, $i, 1)))
+;
}
return ($score / $len);

[download]

That's pretty straightforward, but also pretty slow. The strings are two aligned aminoacid sequences like this one:
string1: "EKFCNSVVDLYSNLSKPFLDIVLYIFKLTSAIGAQGPA----SMMAYLVV"
string2: "ERFCRQLSSMASKLI-------ISPFTLVYYTYQCFQSTGWPVSIFGYFI"

[download]

Is there another way to get the percent of identity of such strings like in my simple code above but more efficient and faster?
I found a hint to 'String::Approx' here on Perlmonks, but I don't really know if that's what I need, since it talks about distances and I don't know if that really is comparable to my percentage identity.

Cheerz, Micha

In reply to Similarity of strings by professa

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