/**********************************************************************************
* DNA Sequence Translator 1.0. *
* Copyright (C) 2006 ZIJUAN LIU, YUBO DONG. yubodong@gmail.com *
**********************************************************************************
* This program is free software; you can redistribute it and/or modify *
* it under the terms of the GNU General Public License as published by *
* the Free Software Foundation; either version 2 of the License, or *
* (at your option) any later version. *
* *
* This program is distributed in the hope that it will be useful, *
* but WITHOUT ANY WARRANTY; without even the implied warranty of *
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
* GNU General Public License for more details. *
* *
* You should have received a copy of the GNU General Public License *
* along with this program; if not, write to the Free Software *
* Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA *
* *
**********************************************************************************/
//---------------------------------------------------------------------------------
//Update History
//---------------------------------------------------------------------------------
// Date | Author | Reason
//---------------------------------------------------------------------------------
// 02/25/2006 | Yubo Dong | Created the first version of SEQTranslator
//---------------------------------------------------------------------------------
//
//Class for DNA Sequence Translator
//
function SEQTranslator(){
//
// m_strSEQ stores the after-cleanup DNA sequence.
// m_strSEQProcessed stores the Amino Acid Code for the after-cleanup DNA sequence
//
var m_strSEQ = null,m_strSEQProcessed = null;
this.process = process;
this.getResult = getResult;
this.display = display;
this.getCodonTable = getCodonTable;
this.reverseSEQ = reverseSEQ;
//
// Codon table from http://www.kazusa.or.jp/java/codon_table_java/
//
var m_arrMapping = new Array(
"ATG","M","Met", "ATC","I","Ile", "ATA","I","Ile", "ATT","I","Ile", "ACA","T","THR", "ACT","T","Thr",
"ACG","T","Thr", "ACC","T","Thr", "AAT","N","Asn", "AAC","N","Asn", "AAA","K","Lys", "AAG","K","Lys",
"AGT","S","Ser", "AGC","S","Ser", "AGA","R","Arg", "AGG","R","Arg", "TTT","F","Phe", "TTC","F","Phe",
"TTA","L","Leu", "TTG","L","Leu", "TCA","S","Ser", "TCT","S","Ser", "TCG","S","Ser", "TCC","S","Ser",
"TAG","*","***", "TAA","*","***", "TAC","Y","Tyr", "TAT","Y","Tyr", "TGT","C","Cys", "TGC","C","Cys",
"TGG","W","Trp", "TGA","*","***", "GTG","V","Val", "GTC","V","Val", "GTA","V","Val", "GTT","V","Val",
"GCA","A","Ala", "GCT","A","Ala", "GCG","A","Ala", "GCC","A","Ala", "GAT","D","Asp", "GAC","D","Asp",
"GAG","E","Glu", "GAA","E","Glu", "GGA","G","Gly", "GGT","G","Gly", "GGG","G","Gly", "GGC","G","Gly",
"CTG","L","Leu", "CTA","L","Leu", "CTT","L","Leu", "CTC","L","Leu", "CCT","P","Pro", "CCA","P","Pro",
"CCC","P","Pro", "CCG","P","Pro", "CAT","H","His", "CAC","H","His", "CAA","Q","Gln", "CAG","Q","Gln",
"CGA","R","Arg", "CGT","R","Arg", "CGG","R","Arg", "CGC","R","Arg");
function getCodonTable(){return m_arrMapping;}
function process(seq, one_three){
m_strSEQ = seq;
var strProcessedSEQ = seq.toUpperCase();
strProcessedSEQ = preProcessSEQ(strProcessedSEQ);
strProcessedSEQ = processHelper(strProcessedSEQ, one_three);
if ( strProcessedSEQ == null ) return null;
m_strSEQProcessed = strProcessedSEQ;
var obj = postProcess(strProcessedSEQ);
return obj;
}
function preProcessSEQ(str){
//Remove all space
str = str.replace(/ /g,'');
str = str.replace(/\n/g,'');
str = str.replace(/\r/g,'');
str = str.replace(/\t/g,'');
//Replace all Us with Ts
str = str.replace(/U/g,'T');
//Remove all non A,T,G,C character
var strExceptional="BDEFHIJKLMNOPQRSUVWXYZ0123456789";
for ( var i = 0; i < strExceptional.length; i ++ ){
eval("str = str.replace(/" + strExceptional.charAt(i) + "/g,'');");
}
//Remove all special character
str = str.replace(/[/]/g,'');
str = str.replace(/[\"\']/g,'');
str = str.replace(/[.]/g,'');
str = str.replace(/[(]/g,'');
str = str.replace(/[)]/g,'');
str = str.replace(/[_~!`+-=;:\[\]\{\}\|\\@#\$%^&\*,\?<>]/g,'');
m_strSEQ = str;
return str;
}
//
//Reverse the DNA sequence and turn all As to Ts , all Ts to As, all Cs to Gs and all Gs to Cs
//
function reverseSEQ(seq){
var newSEQ = "";
for ( var i = seq.length - 1; i >= 0; i -- ){
var ch = seq.charAt(i);
switch (ch){
case 'A': ch = 'T'; break;
case 'T': ch = 'A'; break;
case 'G': ch = 'C'; break;
case 'C': ch = 'G'; break;
default: ch = ""; break;
}
newSEQ += ch;
}
return newSEQ;
}
//
//Look up codon database for given codon
//
function lookupCodon(strCodon){
var obj = null;
for ( var i = 0; i < m_arrMapping.length; i += 3 ){
if ( strCodon == m_arrMapping[i] ){
obj = new Object();
obj.one = m_arrMapping[i+1];
obj.three = m_arrMapping[i+2];
break;
}
}
return obj;
}
function processHelper(seq, one_or_three){
//Looking for ATG
var iIndex = seq.indexOf("ATG");
//If to ATG was found in original sequence, reverse the original sequence and re-look again.
if ( iIndex == -1 ) seq = reverseSEQ(seq);
iIndex = seq.indexOf("ATG");
if ( iIndex == -1 ){
alert("Sorry, unrecognized DNA sequence!");
return null;
}
var newSEQ = "";
seq = seq.substr(iIndex, seq.length - iIndex);
m_strSEQ = seq;
for ( var i = 0; i < seq.length; i += 3 ){
var tmpSEQ = seq.substr(i,3);
var obj = lookupCodon(tmpSEQ);
if ( obj == null ) newSEQ += " ";
else{
if ( one_or_three )
newSEQ += " " + obj.one + " ";
else
newSEQ += obj.three;
}
}
return newSEQ;
}
function postProcess(strSEQ){
var strSEQOriginal = "", strSEQProcessed = "";
for ( var i = 0; i < m_strSEQ.length; i += 3 ){
var tmpSEQ = m_strSEQ.substr(i,3);
strSEQOriginal += tmpSEQ + " ";
tmpSEQ = strSEQ.substr(i,3);
strSEQProcessed += tmpSEQ + " ";
}
var obj = new Object();
obj.original = strSEQOriginal;
obj.processed = strSEQProcessed;
return obj;
}
function getResult(){
if ( m_strSEQProcessed == null ) return null;
var obj = new Object();
obj.original = m_strSEQ;
obj.processed = m_strSEQProcessed;
return obj;
}
function padNumber(iNum, len){
var strNum = iNum + "";
var newStr="";
for ( var i = 0; i < len - strNum.length; i ++ )
newStr += " ";
return newStr + strNum;
}
function display(e, obj){
var str = "";
str += "SEQTranslator 1.0 All rights reserved. Contact: ziliu@med.wayne.edu";
str += "
";
var strHTML = str + "";
var iNumOriginal = 1, iNumProcessed = 1;
strHTML += "";
strHTML += padNumber(1, 8) + padNumber(5, 5) + padNumber(10, 8) + padNumber(15, 6) + padNumber(20, 7);
strHTML += padNumber(25, 7) + padNumber(30, 6) + padNumber(35, 7) + padNumber(40, 7) + padNumber(45, 6);
strHTML += padNumber(50, 7) + padNumber(55, 7) + padNumber(60, 6);
strHTML += "
";
for ( var i = 0; i < obj.original.length; i += 80 ){
var tmpSEQ1 = obj.original.substr(i,80);
var tmpSEQ2 = obj.processed.substr(i,80);
tmpSEQ1 = "" + padNumber(iNumOriginal, 5) + ": " + tmpSEQ1.replace(/ /g," ") + "";
tmpSEQ2 = "" + padNumber(iNumProcessed, 5) + ": " + tmpSEQ2.replace(/ /g," ") + "";
strHTML += tmpSEQ1 + "
";
strHTML += tmpSEQ2 + "
";
iNumOriginal += 60;
iNumProcessed += 20;
}
strHTML += "
";
e.innerHTML = strHTML;
}
}