Input sequence\n\n$sequence
";
// In next lines, the DNA code will be colored and output
$dna=chunk_split($dna,60,'
');
// just to put a bit of color
$color="red"; // or blue, green, white, black, magenta...
$dna=preg_replace("/A/","A",$dna);
$dna=preg_replace("/C/","C",$dna);
$dna=preg_replace("/G/","G",$dna);
$dna=preg_replace("/T/","T",$dna);
// two lines to reduce the code to be transmitted
$dna=preg_replace("/<\/font>/","",$dna);
$dna=preg_replace("/<\/font> /"," ",$dna);
// print DNA code
print "Reverse Translated sequence\n\n$dna";
// ########################## FUNTIONS ############################################
function translate_protein_to_DNA($seq,$genetic_code){
// $aminoacids is the array of aminoacids
$aminoacids=array("(F )","(L )","(I )","(M )","(V )","(S )","(P )","(T )","(A )","(Y )",
"(\* )","(H )","(Q )","(N )","(K )","(D )","(E )","(C )","(W )","(R )",
"(G )","(X )");
// $triplets is the array containning the genetic codes
// Info has been extracted from http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode
// Standard genetic code
$triplets[1]=array("TTY","YTN","ATH","ATG","GTN","WSN","CCN","ACN","GCN","TAY",
"TRR","CAY","CAR","AAY","AAR","GAY","GAR","TGY","TGG","MGN",
"GGN","NNN");
// Vertebrate Mitochondrial
$triplets[2]=array("TTY","YTN","ATY","ATR","GTN","WSN","CCN","ACN","GCN","TAY",
"WRR","CAY","CAR","AAY","AAR","GAY","GAR","TGY","TGR","CGN",
"GGN","NNN");
// Yeast Mitochondrial
$triplets[3]=array("TTY","TTR","ATY","ATR","GTN","WSN","CCN","MYN","GCN","TAY",
"TAR","CAY","CAR","AAY","AAR","GAY","GAR","TGY","TGR","MGN",
"GGN","NNN");
// Mold, Protozoan and Coelenterate Mitochondrial. Mycoplasma, Spiroplasma
$triplets[4]=array("TTY","YTN","ATH","ATG","GTN","WSN","CCN","ACN","GCN","TAY",
"TAR","CAY","CAR","AAY","AAR","GAY","GAR","TGY","TGR","MGN",
"GGN","NNN");
// Invertebrate Mitochondrial
$triplets[5]=array("TTY","YTN","ATY","ATR","GTN","WSN","CCN","WSN","GCN","TAY",
"TAR","CAY","CAR","AAY","AAR","GAY","GAR","TGY","TGR","CGN",
"GGN","NNN");
// Ciliate Nuclear; Dasycladacean Nuclear; Hexamita Nuclear
$triplets[6]=array("TTY","YTN","ATH","ATG","GTN","WSN","CCN","ACN","GCN","TAY",
"TGA","CAY","YAR","AAY","AAR","GAY","GAR","TGY","TGG","MGN",
"GGN","NNN");
// Echinoderm Mitochondrial
$triplets[9]=array("TTY","YTN","ATH","ATG","GTN","WSN","CCN","WCN","GCN","TAY",
"TAR","CAY","CAR","AAH","AAG","GAY","GAR","TGY","TGR","CGN",
"GGN","NNN");
// Euplotid Nuclear
$triplets[10]=array("TTY","YTN","ATH","ATG","GTN","WSN","CCN","ACN","GCN","TAY",
"TAR","CAY","CAR","AAY","AAR","GAY","GAR","TGH","TGG","MGN",
"GGN","NNN");
// Bacterial and Plant Plastid
$triplets[11]=array("TTY","YTN","ATH","ATG","GTN","WSN","CCN","ACN","GCN","TAY",
"TRR","CAY","CAR","AAY","AAR","GAY","GAR","TGY","TGG","MGN",
"GGN","NNN");
// Alternative Yeast Nuclear
$triplets[12]=array("TTY","YTN","ATH","ATG","GTN","HBN","CCN","ACN","GCN","TAY",
"TRR","CAY","CAR","AAY","AAR","GAY","GAR","TGY","TGG","MGN",
"GGN","NNN");
// Ascidian Mitochondrial
$triplets[13]=array("TTY","YTN","ATY","ATR","GTN","WSN","CCN","ACN","GCN","TAY",
"TAR","CAY","CAR","AAY","AAR","GAY","GAR","TGY","TGR","CGN",
"RGN","NNN");
// Flatworm Mitochondrial
$triplets[14]=array("TTY","YTN","ATH","ATG","GTN","WSN","CCN","ACN","GCN","TAH",
"TAG","CAY","CAR","ATH","AAG","GAY","GAR","TGY","TGR","CGN",
"GGN","NNN");
// Blepharisma Macronuclear
$triplets[15]=array("TTY","YTN","ATH","ATG","GTN","WSN","CCN","ACN","GCN","TAY",
"TRA","CAY","YAR","AAY","AAR","GAY","GAR","TGY","TGG","MGN",
"GGN","NNN");
// Chlorophycean Mitochondrial
$triplets[16]=array("TTY","YWN","ATH","ATG","GTN","WSN","CCN","ACN","GCN","TAY",
"TRA","CAY","CAR","AAY","AAR","GAY","GAR","TGY","TGG","MGN",
"GGN","NNN");
// Trematode Mitochondrial
$triplets[21]=array("TTY","YTN","ATY","ATR","GTN","WSN","CCN","ACN","GCN","TAY",
"TAR","CAY","CAR","AAH","AAG","GAY","GAR","TGY","TGR","CGN",
"GGN","NNN");
// Scenedesmus obliquus mitochondrial
$triplets[22]=array("TTY","YWN","ATH","ATG","GTN","WSB","CCN","ACN","GCN","TAY",
"TVR","CAY","CAR","AAY","AAR","GAY","GAR","TGY","TGG","MGN",
"GGN","NNN");
// Thraustochytrium mitochondrial code
$triplets[23]=array("TTY","YTN","ATH","ATG","GTN","WSN","CCN","ACN","GCN","TAY",
"TDR","CAY","CAR","AAY","AAR","GAY","GAR","TGY","TGG","MGN",
"GGN","NNN");
// place a space after each aminoacid in the sequence
$temp = chunk_split($seq,1,' ');
// replace aminoacid by corresponding amnoacid
$peptide = preg_replace ($aminoacids, $triplets[$genetic_code], $temp);
// return peptide sequence
return $peptide;
}
function print_form(){
?>