Well, if @genome were a string, then this would work fairly well and not require keeping track of more variables than needed: 
my ( $ac, $ag, $at, $cc, $cg, $ga, $gc, $ta, $tg, $tt )
  = ( 0, 0, 0, 0, 0, 0, 0, 0, 0, 0  );

my %seq = ( aa => \$tt, ag => \$ag, ac => \$ac, at => \$at,
            ta => \$ta, tg => \$tg, tc => \$ga, tt => \$tt,
            ca => \$tg, cg => \$cg, cc => \$cc, ct => \$ag,
            ga => \$ga, gg => \$cc, gc => \$gc, gt => \$ac
          );

# do some stuff ...

${$seq{$1}}++ while $genome =~ m/(..)/g;

[download]
I don't know how this would compare to the other examples already given, but it's a darn sight better than the original.

In reply to Re: how can I speed up this perl?? by Anonymous Monk
in thread how can I speed up this perl?? by Anonymous Monk

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