# "$ _" is really "$_", and change the qq to a double-quote
  $_ = 
  "CG
  T--A
  A---T
  A----T
   C----G
    T----A
     A---T
      and 
       so 
       on
  ";
  @_{A => C => G => T => } = 0..3;
  s|.*(\w).*(\w).*\n|$_{$-++ / 9 % 2 ? $2:$ 1}|gex;
  s|(.)(.)(.)(.)|chr (64*$1 + 16*$2 + 4*$3 + $4)|gex;
  eval
[download]

  @_{A => C => G => T => } = 0..3;
  # is really...
  @_{'A', 'C', 'G', 'T'}   = 0..3;
[download]

The next line of code transforms the chromosome into a series of Base4 digits, by substituting the appropriate digit for each line:

  s|
    .*      # greedily match
    (\w)    # match first letter, and store into $1
    .*      # greedily match
    (\w)    # match last letter, and store into $2
    .*\n    # eat up remainder of line
  |
    # this expression maps the relevant character to its Base4 digit f
+rom 
    # the %_ hash. The $- is used as a line counter (it defaults to 0)
+. When 
    # the DNA strands flip positions, this continues decoding on the c
+orrect
    # strand (see physi's comment for a visual representation of this)
    $_{$-++ / 9 % 2 ? $2:$ 1}
  |gex;
[download]

  s|
    # store next four characters into $1,$2,$3, and $4
    (.)(.)(.)(.)
  |
    # replace with a Base4-to-ASCII conversion of those characters
    chr (64*$1 + 16*$2 + 4*$3 + $4)
  |gex;
[download]

And, in case anyone's interested, here's the corresponding Perl-to-DNA encoder:

use strict;

my $BASE = 4;
my %NUC_PAIRS = (
  A => T =>
  C => G =>
  G => C =>
  T => A =>
);
my @DIGIT_TO_NUC = qw( A C G T );
my $FMT_DNA = <<END;
 01
0--1
0---1
0----1
 0----1
  0---1
   0--1
    01
    10
   1--0
  1---0
 1----0
1----0
1---0
1--0
 10
END
my @FMT_DNA = split "\n",$FMT_DNA;

my $str = 'print"Just Another Perl Hacker\n"';

my @str_digits;
for (split//, $str) {
  my $ord = ord($_);
  my @digits = (0) x 4;
  print "$ord:\t";
  my $i = 0;
  while ($ord) {
    $digits[4 - ++$i] = $ord % $BASE;
    $ord = int ($ord / $BASE);
  }
  print "@digits\n";
  push @str_digits, [@digits];
}

my $i = 0;
for (@str_digits) {
  for (@$_) {
    my $fmt     = $FMT_DNA[$i++ % @FMT_DNA];
    my $nuc0 = $DIGIT_TO_NUC[$_];
    my $nuc1 = $NUC_PAIRS{$nuc0};
    $fmt =~ s/0/$nuc0/;
    $fmt =~ s/1/$nuc1/;
    print "$fmt\n";
  }
}
[download]

   MeowChow                                   
               s aamecha.s a..a\u$&owag.print

Sorry my ignorance... But I REALLY did not understand this part of the code:

 my $fmt = $FMT_DNA[$i++ % @FMT_DNA];

I searched in books on "%" and nothing there helped me to understand its functioning here...

Please... Give me your wisdom Saint Monk...

Braz Monk

%: Modolus operator. If $a % $b, returns the remainder when $a is divided by $b. Thus, 45 % 6 is 3, as is 51 % 6.

The code in question does this:

my $fmt = $FMT_DNA[$i++ % @FMT_DNA];
[download]

1. Get the remainder when $i is divided by the number of elements in @FMT_DNA and put it in a temp variable.
2. Increment $i by 1.
3. Get the element in @FMT_DNA with an index of the temp variable and put it in $fmt.

What this is doing is treating @FMT_DNA as a circular list - a list that will wrap around to the beginning when it runs out of elements. So, if it was 3 elements, it would do element 0, element 1, element 2, element 0, element 1, etc.

------
We are the carpenters and bricklayers of the Information Age.

The idea is a little like C++ templates, except not quite so brain-meltingly complicated. -- TheDamian, Exegesis 6

Please remember that I'm crufty and crochety. All opinions are purely mine and all code is untested, unless otherwise specified.

how do u decode a computer code called Base4 used to substitute numbers for letters of the alphabet?

CG
T--A
A---T
 A----T
  C----G
   T----A
    A---T
     G--C
      CG
      CG
     C--G
    G---C
   G----C
  C----G
A----T
C---G
G--C
  AT
   CG
   A--T

And now I see that there IS a deeper sense :-) Congrat.
Maybe this is the first step to write a perl program which make changes to itselfe and see what's gonna happen. So there is maybe a chance, that this perl program becomes a perl Operating System one day ...
ok, stop dreaming but keep on hoping :)

-----------------------------------
--the good, the bad and the physi--
-----------------------------------
[download]

A prettiest obfuscated code contest anyone?