BioPHP - Protein to DNA reverse translation
Original code submitted by josebaCode bellow is covered by GNU GPL v2 license.
Description
Last change: 2011/04/27 11:01 | Recent Changes | Original descriptionEnter a protein sequence and obtain its reverse translation. Useful in design of degenerate oligonucleotides. All genetic codes are available.
Code
Last change: 2011/04/27 11:01 | Recent Changes | Download | Original code and
<html><head><title>Protein to DNA reverse translation</title>
</head><body bgcolor=white text=black>
<?php
// author Joseba Bikandi
// license GNU GPL v2
error_reporting(0);
//If nothing is posted, print form and die
if (!$_POST){print_form();die();} // from is in the bottom
// IF INFO IS POSTED, GO AHEAD
// Get the sequence
$sequence = strtoupper($_POST["sequence"]);
// remove non-coding chacacters
$sequence = preg_replace ("([^FLIMVSPTAY*HQNKDECWRGX\*])", "", $sequence);
$len=strlen($sequence);
// Get the genetic code to be used for translation
$genetic_code = $_POST["genetic_code"];
// Translate in 5-3 direction
$dna=translate_protein_to_DNA($sequence, 1);
$sequence=chunk_split($sequence,20);
print "<pre><font size=+1>Input sequence\n\n$sequence<hr>";
// In next lines, the DNA code will be colored and output
$dna=chunk_split($dna,60,'<br>');
// just to put a bit of color
$color="red"; // or blue, green, white, black, magenta...
$dna=preg_replace("/A/","<font color=".$color.">A</font>",$dna);
$dna=preg_replace("/C/","<font color=".$color.">C</font>",$dna);
$dna=preg_replace("/G/","<font color=".$color.">G</font>",$dna);
$dna=preg_replace("/T/","<font color=".$color.">T</font>",$dna);
// two lines to reduce the code to be transmitted
$dna=preg_replace("/<\/font><font color=$color>/","",$dna);
$dna=preg_replace("/<\/font> <font color=$color>/"," ",$dna);
// print DNA code
print "Reverse Translated sequence\n\n$dna</font>";
// ########################## 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(){
?>
<center>
<form name=mydna method=post action="<? print $_SERVER["PHP_SELF"]; ?>">
<h2>Protein to DNA reverse translation</h2>
Protein sequence<br>
<textarea name=sequence cols=75 rows=10>
FLIMVSPTAYHQNKDECWRGX*
</textarea>
<br>
Genetic code: <select name=genetic_code>
<option value=1 selected>Standard
<option value=2>Vertebrate Mitochondrial
<option value=3>Yeast Mitochondrial
<option value=4>Mold, Protozoan and Coelenterate Mitochondrial. Mycoplasma, Spiroplasma
<option value=5>Invertebrate Mitochondrial
<option value=6>Ciliate Nuclear; Dasycladacean Nuclear; Hexamita Nuclear
<option value=9>Echinoderm Mitochondrial
<option value=10>Euplotid Nuclear
<option value=11>Bacterial and Plant Plastid
<option value=12>Alternative Yeast Nuclear
<option value=13>Ascidian Mitochondrial
<option value=14>Flatworm Mitochondrial
<option value=15>Blepharisma Macronuclear
<option value=16>Chlorophycean Mitochondrial
<option value=21>Trematode Mitochondrial
<option value=22>Scenedesmus obliquus mitochondrial
<option value=23>Thraustochytrium mitochondrial code
</select>
<P>
<input type=submit value=" Translate to DNA ">
<hr width=500>
Source code available at <a href=http://www.biophp.org/minitools/protein_to_dna>biophp.org</a>
<p>
<div align=right><a href="../dna_to_protein/index.php">DNA to Protein</a></div>
<? } ?>
<hr>
Source code available at <a href=http://www.biophp.org/minitools/protein_to_dna>biophp.org</a>
</body></html>