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BioPHP - Protein to DNA reverse translation

Original code submitted by joseba
Code bellow is covered by GNU GPL v2 license.

Description

Last change: 2010/10/18 17:04 | Edit description | Recent Changes | Original description

Reverse translation of protein to DNA by using one fo the 13 genomic codes
described.

Code

Last change: 2010/10/18 17:04 | Edit Code | Recent Changes | Download | Original code

function 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;

}