Use the XOR! 

my $x = "EKFCNSVVDLYSNLSKPFLDIVLYIFKLTSAIGAQGPA----SMMAYLVV";
my $y = "ERFCRQLSSMASKLI-------ISPFTLVYYTYQCFQSTGWPVSIFGYFI";
my $z = $x^$y;
my $score = ($z =~ tr/\0//);
return $score/length($x)

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In reply to Re: Similarity of strings by ariels
in thread Similarity of strings by professa

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