If I understand the Trypsin example (I have no knowledge of this problem domain) the following code leverages Perl's string handling to produce the results I think you are looking for in this narrow case.

use strict;
use warnings;

my $str = 'GVGFTVILISFKYVGFFYNVIIAWALHYFFSSFTMDLPRWIHCNNTWNSPNCSDAHASN
+SSDGLGLNDTFGTTPAAEYFER';
my @segments = map {[$_, (scalar tr/STY//)]} split /(?<=[KR])/, $str;

printf "%45s: %d\n", @$_ for @segments;

[download]

Prints:

                                 GVGFTVILISFK: 2
                  YVGFFYNVIIAWALHYFFSSFTMDLPR: 6
   WIHCNNTWNSPNCSDAHASNSSDGLGLNDTFGTTPAAEYFER: 10

[download]

I've no idea how the performance may compare with whatever you are doing now, but if this does anything like the task you need then I'm sure it will be an order of magnitude faster than a character at a time implementation.

True laziness is hard work

In reply to Re^2: Efficient walk/iterate along a string by GrandFather
in thread Efficient walk/iterate along a string by gje21c

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