// Reverse translation
function split(x,n)
{
var y = new Array();
var str = x.length/n;
for (var i = 0; i < str; i++) {
y[i] = x.substring(i*n,n+i*n) + "
";
}
return y;
}
function atransl()
{
treelett = new Array("arg","leu","ser","thr","pro","ala","gly","val","lys","asn","gln","his","glu","asp","tyr","cys","phe","ile","met","trp","***","end","???");
onelett = new Array("r","l","s","t","p","a","g","v","k","n","q","h","e","d","y","c","f","i","m","w","*","*","?");
treelett_out = new Array("Arg","Leu","Ser","Thr","Pro","Ala","Gly","Val","Lys","Asn","Gln","His","Glu","Asp","Tyr","Cys","Phe","Ile","Met","Trp","***","End","???");
nucl = new Array("mng","yun","wsn","acn","ccn","gcn","ggn","gun","aar","aay","car","cay","gar","gay","uay","ugy","uuy","auh","aug","ugg","urr","urr","???");
ncode = "r=a,g k=g,u h=a,c,u d=a,g,u
y=c,t s=c,g b=c,g,u n=a,g,c,u
m=a,c w=a,u v=a,c,g";
if(document.rtransl.u_t[1].checked) ncode = ncode.replace(/u/g,"t");
if(document.rtransl.ftnt[1].checked) ncode = ncode.toUpperCase();
switch ( document.rtransl.org.selectedIndex )
{
case 1:
organism = "Mus musculus";
freq_a = new Array(43,0,39,100,0, 0,0,0,100,100, 0,0,0,0,0, 0,0,100,100,0, 0,0,
0,0,0,0,0, 0,0,0,100,100, 100,100,100,100,100, 0,0,0,0,0, 52,52,
33,14,14,29,28, 23,26,12,39,0, 25,0,40,0,0, 0,0,16,0,0, 76,76);
freq_g = new Array(0,0,0,0,0, 100,100,100,0,0, 0,0,100,100,0, 0,0,0,0,0, 0,0,
100,0,39,0,0, 0,100,0,0,0, 0,0,0,0,0, 100,0,0,0,100, 48,48,
41,53,5,11,10, 10,23,46,61,0, 75,0,60,0,0, 0,0,0,100,100, 24,24);
freq_c = new Array(57,80,0,0,100, 0,0,0,0,0, 100,100,0,0,0, 0,0,0,0,0, 0,0,
0,0,61,100,100, 100,0,0,0,0, 0,0,0,0,0, 0,0,0,0,0, 0,0,
17,20,46,35,31, 38,33,25,0,57, 0,60,0,56,57, 52,56,50,0,0, 0,0);
freq_u = new Array(0,20,61,0,0, 0,0,0,0,0, 0,0,0,0,100, 100,100,0,0,100, 100,100,
0,100,0,0,0, 0,0,100,0,0, 0,0,0,0,0, 0,100,100,100,0, 0,0,
9,13,35,25,31, 29,18,17,0,43, 0,40,0,44,43, 48,44,34,0,0, 0,0);
break;
case 2:
organism = "Drosophila melanogaster";
freq_a = new Array(21,0,39,100,0, 0,0,0,100,100, 0,0,0,0,0, 0,0,100,100,0, 0,0,
0,0,0,0,0, 0,0,0,100,100, 100,100,100,100,100, 0,0,0,0,0, 74,74,
25,14,9,20,25, 17,28,11,30,0, 30,0,33,0,0, 0,0,19,0,0, 68,68);
freq_g = new Array(0,0,0,0,0, 100,100,100,0,0, 0,0,100,100,0, 0,0,0,0,0, 0,0,
100,0,39,0,0, 0,100,0,0,0, 0,0,0,0,0, 100,0,0,0,100, 26,26,
26,61,20,26,29, 19,8,47,70,0, 70,0,67,0,0, 0,0,0,100,100, 32,32);
freq_c = new Array(79,77,0,0,100, 0,0,0,0,0, 100,100,0,0,0, 0,0,0,0,0, 0,0,
0,0,61,100,100, 100,0,0,0,0, 0,0,0,0,0, 0,0,0,0,0, 0,0,
33,15,48,38,33, 45,43,24,0,55, 0,60,0,47,63, 71,62,47,0,0, 0,0);
freq_u = new Array(0,23,61,0,0, 0,0,0,0,0, 0,0,0,0,100, 100,100,0,0,100, 100,100,
0,100,0,0,0, 0,0,100,0,0, 0,0,0,0,0, 0,100,100,100,0, 0,0,
16,10,22,17,13, 19,21,18,0,45, 0,40,0,53,37, 29,38,34,0,0, 0,0);
break;
case 3:
organism = "Arabidopsis thaliana";
freq_a = new Array(55,0,28,100,0, 0,0,0,100,100, 0,0,0,0,0, 0,0,100,100,0, 0,0,
0,0,0,0,0, 0,0,0,100,100, 100,100,100,100,100, 0,0,0,0,0, 56,56,
47,24,20,31,33, 27,37,15,49,0, 56,0,52,0,0, 0,0,24,0,0, 80,80);
freq_g = new Array(0,0,0,0,0, 100,100,100,0,0, 0,0,100,100,0, 0,0,0,0,0, 0,0,
100,0,28,0,0, 0,100,0,0,0, 0,0,0,0,0, 100,0,0,0,100, 44,44,
29,33,10,15,18, 14,15,26,51,0, 44,0,48,0,0, 0,0,0,100,100, 20,20);
freq_c = new Array(45,64,0,0,100, 0,0,0,0,0, 100,100,0,0,0, 0,0,0,0,0, 0,0,
0,0,72,100,100, 100,0,0,0,0, 0,0,0,0,0, 0,0,0,0,0, 0,0,
7,17,25,20,11, 16,14,19,0,48, 0,39,0,32,48, 40,49,35,0,0, 0,0);
freq_u = new Array(0,36,72,0,0, 0,0,0,0,0, 0,0,0,0,100, 100,100,0,0,100, 100,100,
0,100,0,0,0, 0,0,100,0,0, 0,0,0,0,0, 0,100,100,100,0, 0,0,
17,26,44,34,38, 43,34,41,0,52, 0,61,0,68,52, 60,51,41,0,0, 0,0);
break;
case 4:
organism = "Saccharomyces cerevisiae";
freq_a = new Array(69,0,27,100,0, 0,0,0,100,100, 0,0,0,0,0, 0,0,100,100,0, 0,0,
0,0,0,0,0, 0,0,0,100,100, 100,100,100,100,100, 0,0,0,0,0, 68,68,
55,42,21,30,41, 29,22,21,58,0, 69,0,70,0,0, 0,0,27,0,0, 77,77);
freq_g = new Array(0,0,0,0,0, 100,100,100,0,0, 0,0,100,100,0, 0,0,0,0,0, 0,0,
100,0,27,0,0, 0,100,0,0,0, 0,0,0,0,0, 100,0,0,0,100, 32,32,
25,40,10,14,12, 11,12,19,42,0, 31,0,30,0,0, 0,0,0,100,100, 23,23);
freq_c = new Array(31,44,0,0,100, 0,0,0,0,0, 100,100,0,0,0, 0,0,0,0,0, 0,0,
0,0,73,100,100, 100,0,0,0,0, 0,0,0,0,0, 0,0,0,0,0, 0,0,
6,6,27,22,16, 22,19,21,0,41, 0,36,0,35,44, 37,41,26,0,0, 0,0);
freq_u = new Array(0,56,73,0,0, 0,0,0,0,0, 0,0,0,0,100, 100,100,0,0,100, 100,100,
0,100,0,0,0, 0,0,100,0,0, 0,0,0,0,0, 0,100,100,100,0, 0,0,
14,13,42,34,31, 38,47,39,0,59, 0,64,0,65,56, 63,59,46,0,0, 0,0);
break;
case 5:
organism = "Pichia pastoris";
freq_a = new Array(64,0,25,100,0, 0,0,0,100,100, 0,0,0,0,0, 0,0,100,100,0, 0,0,
0,0,0,0,0, 0,0,0,100,100, 100,100,100,100,100, 0,0,0,0,0, 82,82,
58,28,19,24,41, 23,32,15,47,0, 61,0,57,0,0, 0,0,19,0,0, 71,71);
freq_g = new Array(0,0,0,0,0, 100,100,100,0,0, 0,0,100,100,0, 0,0,0,0,0, 0,0,
100,0,25,0,0, 0,100,0,0,0, 0,0,0,0,0, 100,0,0,0,100, 18,18,
20,48,9,11,9, 6,10,19,53,0, 39,0,43,0,0, 0,0,0,100,100, 29,29);
freq_c = new Array(36,51,0,0,100, 0,0,0,0,0, 100,100,0,0,0, 0,0,0,0,0, 0,0,
0,0,75,100,100, 100,0,0,0,0, 0,0,0,0,0, 0,0,0,0,0, 0,0,
5,8,29,25,15, 26,14,23,0,51, 0,43,0,42,54, 35,46,32,0,0, 0,0);
freq_u = new Array(0,49,75,0,0, 0,0,0,0,0, 0,0,0,0,100, 100,100,0,0,100, 100,100,
0,100,0,0,0, 0,0,100,0,0, 0,0,0,0,0, 0,100,100,100,0, 0,0,
16,16,44,40,35, 45,44,42,0,49, 0,57,0,58,46, 65,54,50,0,0, 0,0);
break;
case 6:
organism = "Escherichia coli";
freq_a = new Array(13,0,40,100,0, 0,0,0,100,100, 0,0,0,0,0, 0,0,100,100,0, 0,0,
0,0,0,0,0, 0,0,0,100,100, 100,100,100,100,100, 0,0,0,0,0, 70,70,
16,19,15,19,21, 24,15,17,73,0, 34,0,67,0,0, 0,0,14,0,0, 91,91);
freq_g = new Array(0,0,0,0,0, 100,100,100,0,0, 0,0,100,100,0, 0,0,0,0,0, 0,0,
100,0,40,0,0, 0,100,0,0,0, 0,0,0,0,0, 100,0,0,0,100, 30,30,
17,58,13,24,64, 31,16,34,27,0, 66,0,33,0,0, 0,0,0,100,100, 9,9);
freq_c = new Array(87,72,0,0,100, 0,0,0,0,0, 100,100,0,0,0, 0,0,0,0,0, 0,0,
0,0,60,100,100, 100,0,0,0,0, 0,0,0,0,0, 0,0,0,0,0, 0,0,
33,10,38,37,13, 26,35,20,0,48, 0,41,0,36,39, 53,41,37,0,0, 0,0);
freq_u = new Array(0,28,60,0,0, 0,0,0,0,0, 0,0,0,0,100, 100,100,0,0,100, 100,100,
0,100,0,0,0, 0,0,100,0,0, 0,0,0,0,0, 0,100,100,100,0, 0,0,
34,12,34,19,19, 19,34,29,0,52, 0,59,0,64,61, 47,59,49,0,0, 0,0);
break;
default:
organism = "Homo sapiens"
freq_a = new Array(42,0,39,100,0, 0,0,0,100,100, 0,0,0,0,0, 0,0,100,100,0, 0,0,
0,0,0,0,0, 0,0,0,100,100, 100,100,100,100,100, 0,0,0,0,0, 53,53,
32,15,15,28,28, 23,25,12,43,0, 26,0,42,0,0, 0,0,17,0,0, 76,76);
freq_g = new Array(0,0,0,0,0, 100,100,100,0,0, 0,0,100,100,0, 0,0,0,0,0, 0,0,
100,0,39,0,0, 0,100,0,0,0, 0,0,0,0,0, 100,0,0,0,100, 47,47,
41,53,6,11,11, 11,25,46,57,0, 74,0,58,0,0, 0,0,0,100,100, 24,24);
freq_c = new Array(58,80,0,0,100, 0,0,0,0,0, 100,100,0,0,0, 0,0,0,0,0, 0,0,
0,0,61,100,100, 100,0,0,0,0, 0,0,0,0,0, 0,0,0,0,0, 0,0,
19,20,46,36,32, 40,34,24,0,53, 0,58,0,54,56, 55,54,47,0,0, 0,0);
freq_u = new Array(0,20,61,0,0, 0,0,0,0,0, 0,0,0,0,100, 100,100,0,0,100, 100,100,
0,100,0,0,0, 0,0,100,0,0, 0,0,0,0,0, 0,100,100,100,0, 0,0,
8,13,34,24,29, 26,16,18,0,47, 0,42,0,46,44, 45,46,36,0,0, 0,0);
}
// забираем значения, заданные в форме
var aseq = document.rtransl.str.value;
var name_seq = document.rtransl.name.value;
var al = parseFloat(document.rtransl.al.value);
if(isNaN(al)){alert(alt19_01); document.rtransl.al.focus(); return true;};
al = Math.floor(Math.abs(al));
document.rtransl.al.value = al;
// приводим "str" к стандартному виду который будет называться "aseq"
aseq = aseq.toLowerCase();
if(document.rtransl.code[0].checked)
{
aseq = aseq.replace(/[^acdefghiklmnpqrstvwy*]/g,"");
aalength = aseq.length;
if(aalength<1){alert(alt19_02); document.rtransl.str.focus(); return true;};
} else {
aseq = aseq.replace(/[^acdeghilmnoprstuvy*]/g,"");
aalength = aseq.length;
if(aalength<3){alert(alt19_03); document.rtransl.str.focus(); return true;};
aalength = Math.floor(aalength/3);
}
// переводим аминокислотную последовательность в номера, соответствующие индивидуальным аминокислотам
var aa = new Array();
for(var i1 = 0; i1 < aalength; i1++)
{
for(var i2 = 0; i2 < 23; i2++)
{
if(document.rtransl.code[0].checked)
{
if(aseq.substring(i1,i1+1) == onelett[i2]) {aa[i1] = i2; break};
} else {
if(i2 == 22) {aa[i1] = 22; break};
if(aseq.substring(i1*3,i1*3+3) == treelett[i2]) {aa[i1] = i2; break};
}
}
}
codseq = "";
oseq = "";
aseq1 = "";
nseq = new Array("","","","");
function compare(a, b)
{
a1 = Math.floor(a.slice(0,-1));
b1 = Math.floor(b.slice(0,-1));
if ( a1 > b1 ) return -1;
if ( a1 < b1 ) return 1;
return 0;
}
for(var i3 = 0; i3 < aalength; i3++)
{
codseq += (i3 + 1) + "-";
oseq += nucl[aa[i3]];
if(aa[i3] == 22)
{
aseq1 += aseq.substring(i3*3,i3*3+3);
codseq += aseq.substring(i3*3,i3*3+3) + " -- Undefined amino acid\n";
nseq[0] += "???"; nseq[1] += " "; nseq[2] += " "; nseq[3] += " ";
continue;
}
if(document.rtransl.code[0].checked)
{
codseq += onelett[aa[i3]] + "\n";
aseq1 += " " + onelett[aa[i3]] + " ";
} else {
codseq += treelett_out[aa[i3]] + "\n";
aseq1 += treelett_out[aa[i3]];
}
for(var i4 = 0; i4 < 3; i4++)
{
codseq += " ";
fourlett = new Array(freq_a[i4*22 + aa[i3]]+"a", freq_g[i4*22 + aa[i3]]+"g", freq_c[i4*22 + aa[i3]]+"c", freq_u[i4*22 + aa[i3]]+"u" );
fourlett.sort(compare);
for(var i5 = 0; i5 < 4; i5++)
{
proc = fourlett[i5].slice(0,-1);
if(proc > 0)
{
nucleotid = fourlett[i5].slice(-1);
if(document.rtransl.u_t[1].checked) nucleotid = nucleotid.replace(/u/g,"t");
if(document.rtransl.ftnt[1].checked) nucleotid = nucleotid.toUpperCase();
nseq[i5] += nucleotid;
if(proc == 100)
{
codseq += nucleotid;
} else {
codseq += nucleotid + "(" + proc + "%) ";
}
} else {
nseq[i5] += " ";
}
}
codseq += "\n";
}
codseq += "\n";
}
if(document.rtransl.ftnt[1].checked) oseq = oseq.toUpperCase();
document.rtransl.codseq.value = codseq;
Aoseq = split(oseq, al*3);
Aaseq1 = split(aseq1, al*3);
Anseq0 = split(nseq[0], al*3);
Anseq1 = split(nseq[1], al*3);
Anseq2 = split(nseq[2], al*3);
Anseq3 = split(nseq[3], al*3);
aseq2 = "";
aseq3 = "";
for(var i6 = 0; i6 < Aaseq1.length; i6++)
{
aseq2 += "" + Aaseq1[i6] + "
" + Anseq0[i6] + "
" + Anseq1[i6] + "
" + Anseq2[i6] + "
" + Anseq3[i6] + "
";
aseq3 += "" + Aaseq1[i6] + "
" + Aoseq[i6] + "
";
}
id = window.open('','result', config='height=500,width=600,toolbar=no,menubar=yes,scrollbars=yes,resizable=yes,location=no,status=no');
id.document.write(" Reverse Translation ");
id.focus();
id.document.write("Reverse translation
> ");
id.document.write(name_seq);
id.document.write(" R-translated in organism: ");
id.document.write(organism);
id.document.write("
");
id.document.write(aseq2);
id.document.write("One-letter code:
> ");
id.document.write(name_seq);
id.document.write("
");
id.document.write(aseq3);
id.document.write("
");
id.document.write(ncode);
id.document.write("
");
// закрываем окно
id.document.write("