%gc = (
'GCA'=>'A', #Alanine
'GCC'=>'A', #Alanine
'GCG'=>'A', #Alanine
'GCT'=>'A', #Alanine
'AGA'=>'R', #Arginine
'AGG'=>'R', #Arginine
'CGA'=>'R', #Arginine
'CGC'=>'R', #Arginine
'CGG'=>'R', #Arginine
'CGT'=>'R', #Arginine
'AAC'=>'N', #Asparagine
'AAT'=>'N', #Asparagine
'GAC'=>'D', #Aspartic acid
'GAT'=>'D', #Aspartic acid
'TGC'=>'C', #Cysteine
'TGT'=>'C', #Cysteine
'GAA'=>'E', #GlTtamic acid
'GAG'=>'E', #GlTtamic acid
'CAA'=>'Q', #GlTtamine
'CAG'=>'Q', #GlTtamine
'GGA'=>'G', #Glycine
'GGC'=>'G', #Glycine
'GGG'=>'G', #Glycine
'GGT'=>'G', #Glycine
'CAC'=>'H', #Histidine
'CAT'=>'H', #Histidine
'ATA'=>'I', #IsoleTcine
'ATC'=>'I', #IsoleTcine
'ATT'=>'I', #IsoleTcine
'TTA'=>'L', #LeTcine
'TTG'=>'L', #LeTcine
'CTA'=>'L', #LeTcine
'CTC'=>'L', #LeTcine
'CTG'=>'L', #LeTcine
'CTT'=>'L', #LeTcine
'AAA'=>'K', #Lysine
'AAG'=>'K', #Lysine
'ATG'=>'M', #Methionine
'TTC'=>'F', #Phenylalanine
'TTT'=>'F', #Phenylalanine
'CCA'=>'P', #Proline
'CCC'=>'P', #Proline
'CCG'=>'P', #Proline
'CCT'=>'P', #Proline
'AGC'=>'S', #Serine
'AGT'=>'S', #Serine
'TCA'=>'S', #Serine
'TCC'=>'S', #Serine
'TCG'=>'S', #Serine
'TCT'=>'S', #Serine
'ACA'=>'T', #Threonine
'ACC'=>'T', #Threonine
'ACG'=>'T', #Threonine
'ACT'=>'T', #Threonine
'TGG'=>'W', #Tryptophan
'TAC'=>'Y', #Tyrosine
'TAT'=>'Y', #Tyrosine
'GTA'=>'V', #Valine
'GTC'=>'V', #Valine
'GTG'=>'V', #Valine
'GTT'=>'V', #Valine
'TAA'=>'-', #STOP
'TAG'=>'-', #STOP
'TGA'=>'-', #STOP
);
#$dna='TGACATAGTCGTATGATGCGTGATACAGATAGACAC';

#print "Give me a DNA sequence:\n";
#$dna=$ARGV[0];
#chomp $dna;
$/="\n";

open (FIN, "</home/user/perl/dna.txt") or die("Could not open input file");

while (<FIN>)
{
	chomp $_;
	$dna=$dna.$_; #$dna.=$_;
}


@dna=split('',$dna);
#print "@dna\n";#fjsdfhjks
@mrna=@dna;

for ($o=0;$o<=$#mrna;$o++)
{
	if ($mrna[$o] eq 'T')
	{
		$mrna[$o]='U';
	}
	else 
	{$mrna[$o]=$mrna[$o];}
}

$mrna=join('',@mrna);
print "$dna\n";#$mrna\n";

$m2=$dna;
$m2=~s/T/U/g;
#$m2=~s/T/U/;
#print "$m2\n";

$cdna=$dna;
$cdna=~tr/ACTG/TGAC/;
$cdna=reverse($cdna);
#print "$cdna\n";
#%gc

#print "\n$fcodon $gc{$fcodon}\n";
for ($b=0;$b<=2;$b++)
{
	for($a=$b;$a<length($dna)-2;$a=$a+3)
	{
	$codon=substr($dna,$a,3);
	$pep=$pep.$gc{$codon};#print "$gc{$codon}\n";	
	}
	#print "$pep\n";
	@pep[$b]=$pep;
	$pep='';
}
if($pep[2]=~m/(M[A-Z]\-)/g)
	{#print "$1\n";
	}