Good morning. First at all I'd like to rather English is not my native language, so I apologize for any misunderstanding or spelling mistake. Anyhow, I have this code you'll see below, and I want to storage the sequences from three diferent ORF (marcos de lectura for Spanish). I don't know how to do that. But I do know where is my mistake: the variable $protein only storage the last sequence of the loop, i.e., the third ORF. I need all of them in the screen. PD: The code is very long but first, it's the genetic code of a mitochondrion, and second I get it that way. I'll appreciate any kind of help. Thanks since now. 

for ($c=0; $c < 3; $c=$c+1){
    for ($position=$c; $position < length $DNA; $position=$position+1)
+{
    
        $codon=substr($DNA, $position, 3); 
        #print "$codon\n";
                
        if($codon eq 'TTT' or $codon eq 'TTC'){
            #print "el codon $codon codifica para Fenilalanina";
            $position=$position+2;
            $protein=$protein."F";
            }
            
        elsif($codon eq 'GGT' or $codon eq 'GGC'or $codon eq 'GGA'or $
+codon eq 'GGG'){
            #print "el codon $codon codifica para Glicina";
            $position=$position+2;
            $protein=$protein."G";
            }
            
        elsif($codon eq 'GCT' or $codon eq 'GCC'or $codon eq 'GCA'or $
+codon eq 'GCG'){
            #print "el codon $codon codifica para Alanina";
            $position=$position+2;
            $protein=$protein."A";
            }
            
        elsif($codon eq 'TTA' or $codon eq 'TTG' or $codon eq 'CTT' or
+ $codon eq 'CTC' or $codon eq 'CTG' or $codon eq 'CTA'){
            #print "el codon $codon codifica para Leucina";
            $position=$position+2;
            $protein=$protein."L";
            }
            
        elsif($codon eq 'GTT' or $codon eq 'GTC'or $codon eq 'GTA'or $
+codon eq 'GTG'){
            #print "el codon $codon codifica para Valina";
            $position=$position+2;
            $protein=$protein."V";
            }
        
        elsif($codon eq 'ATT' or $codon eq 'ATC'or $codon eq 'ATA'){
            #print "el codon $codon codifica para Isoleucina";
            $position=$position+2;
            $protein=$protein."I";
            }
            
        elsif($codon eq 'CCT' or $codon eq 'CCC'or $codon eq 'CCA'or $
+codon eq 'CCG'){
            #print "el codon $codon codifica para Prolina";
            $position=$position+2;
            $protein=$protein."P";
            }
            
        elsif($codon eq 'TCT' or $codon eq 'TCC'or $codon eq 'TCA'or $
+codon eq 'TCG'){
            #print "el codon $codon codifica para Serina";
            $position=$position+2;
            $protein=$protein."S";
            }
            
        elsif($codon eq 'ACT' or $codon eq 'ACC'or $codon eq 'ACA'or $
+codon eq 'ACG'){
            #print "el codon $codon codifica para Treonina";
            $position=$position+2;
            $protein=$protein."T";
            }
            
        elsif($codon eq 'TGT' or $codon eq 'TGC'){
            #print "el codon $codon codifica para Cisteina";
            $position=$position+2;
            $protein=$protein."C";
            }
            
        elsif($codon eq 'TAT' or $codon eq 'TAC'){
            #print "el codon $codon codifica para Tirosina";
            $position=$position+2;
            $protein=$protein."Y";
            }
            
        elsif($codon eq 'AAT' or $codon eq 'AAC'){
            #print "el codon $codon codifica para Asparagina";
            $position=$position+2;
            $protein=$protein."N";
            }
            
        elsif($codon eq 'CAA' or $codon eq 'CAG'){
            #print "el codon $codon codifica para Glutamina";
            $position=$position+2;
            $protein=$protein."Q";
            }
            
        elsif($codon eq 'GAT' or $codon eq 'GAC'){
            #print "el codon $codon codifica para Ácido aspártico";
            $position=$position+2;
            $protein=$protein."D";
            }
            
        elsif($codon eq 'GAA' or $codon eq 'GAG'){
            #print "el codon $codon codifica para Ácido glutámico";
            $position=$position+2;
            $protein=$protein."E";
            }
            
        elsif($codon eq 'CGT' or $codon eq 'CGC' or $codon eq 'CGA' or
+ $codon eq 'CGG' or $codon eq 'AGA' or $codon eq 'AGG'){
            #print "el codon $codon codifica para Arginina";
            $position=$position+2;
            $protein=$protein."R";
            }
            
        elsif($codon eq 'AAA' or $codon eq 'AAG'){
            #print "el codon $codon codifica para Lisina";
            $position=$position+2;
            $protein=$protein."K";
            }
            
        elsif($codon eq 'CAT' or $codon eq 'CAC'){
            #print "el codon $codon codifica para Histidina";
            $position=$position+2;
            $protein=$protein."H";
            }
            
        elsif($codon eq 'TGG' or $codon eq 'TGA' ){
            #print "el codon $codon codifica para Triptofano";
            $position=$position+2;
            $protein=$protein."W";
            }
            
        elsif($codon eq 'ATG'){
            #print "el codon $codon codifica para Metionina";
            $position=$position+2;
            $protein=$protein."M";
            #++$M;
            }
            
        elsif($codon eq 'TAA' or $codon eq 'TAG'){
            #print "el codon $codon codifica para STOP";
            $position=$position+2;
            $protein=$protein."8";
            #++$ZZ;
            }
        
        else {
        #print "codon $codon no es reconocido \n";
        $protein=$protein."x";
        #++$x;
        }
    }
    @marcos=<,$protein>;
    foreach $mar(@marcos){
    print "La secuencia ",$c," es: ",$mar,"\n\n";
    }
}

[download]

In reply to Storage of proteins from diferent ORF by dmunoze

Title:
Use:  <p> text here (a paragraph) </p>
and:  <code> code here </code>
to format your post, it's "PerlMonks-approved HTML":


  • Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!
  • Titles consisting of a single word are discouraged, and in most cases are disallowed outright.
  • Read Where should I post X? if you're not absolutely sure you're posting in the right place.
  • Please read these before you post! —
  • Posts may use any of the Perl Monks Approved HTML tags:
    a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, details, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, summary, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr
  • You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)
            For:     Use:
    & &amp;
    < &lt;
    > &gt;
    [ &#91;
    ] &#93;
  • Link using PerlMonks shortcuts! What shortcuts can I use for linking?
  • See Writeup Formatting Tips and other pages linked from there for more info.