substr($str, $start_idx, $length) =
   '<b>' . substr($str, $start_idx, $length) . '</b>';

##</code><code>##

my $index = 0;
my $replace = "<b>$seq</b>";
while (($index = rindex($str, $seq, $index)) >= 0) {
   substr($str, $index, length($seq)) = $replace;
}