I don't know if this is faster but you could try substr with references, for example: 

for my $i ( 0 .. $max ) {
  my $c = \substr( $protein, $i, 1 );
  # Process $$c etc etc
}

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

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