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/* define the standard genetic code */
/* AAA,AAC,AAG....TTA,TTC,TTG,TTT - 64 all in all*/
_Genetic_Code = {
{14,13,14,13,7,7,7,7,19, 5,19, 5,2,2,3,2,
12,11,12,11,6,6,6,6,19,19,19,19,1,1,1,1,
16,15,16,15,8,8,8,8,20,20,20,20,4,4,4,4,
10,9, 10,9, 5,5,5,5,10,17,18,17,1,0,1,0}
};
/*
here's how codes translate to aminoacids
0 == Phe
1 == Leu
2 == Ile
3 == Met
4 == Val
5 == Ser
6 == Pro
7 == Thr
8 == Ala
9 == Tyr
10 == Stop
11 == His
12 == Gln
13 == Asn
14 == Lys
15 == Asp
16 == Glu
17 == Cys
18 == Trp
19 == Arg
20 == Gly
*/
MG94_1 = {61,61};
MG94_2 = {61,61};
NICETY_LEVEL = 3;
/* a flag to control Mac version responsiveness */
/* defines a sparse transition probabilities matrix
now we'll go through the matrix and assign the elements based on syn/non-syn status*/
hshift = 0;
for (h=0; h<64; h=h+1)
{
if ((h==56)||(h==50)||(h==48))
{
hshift = hshift+1;
continue;
}
vshift = hshift;
for (v = h+1; v<64; v=v+1)
{
/*first check to see if the transition is one step*/
diff = v-h;
/*if the diff is less than 4 then there is a change in the 3rd slot only
if the diff is divisible by 4 but not by 16 then there is a change in the 2nd slot only
if the diff is divisible by 16 then there is a change in the 1st slot only
*/
if ((v==56)||(v==50)||(v==48))
{
vshift = vshift+1;
continue;
}
if ((h$4==v$4)||((diff%4==0)&&(h$16==v$16))||(diff%16==0))
/* the transition is one-step and now we will determine whether it is syn or non-syn */
{
if (h$4==v$4)
{
transition = v%4;
transition2= h%4;
}
else
{
if(diff%16==0)
{
transition = v$16;
transition2= h$16;
}
else
{
transition = v%16$4;
transition2= h%16$4;
}
}
if (_Genetic_Code[0][h]==_Genetic_Code[0][v])
{
MG94_1[h-hshift][v-vshift] := synRate*observedFreq1__[transition__][0];
MG94_1[v-vshift][h-hshift] := synRate*observedFreq1__[transition2__][0];
MG94_2[h-hshift][v-vshift] := synRate*observedFreq2__[transition__][0];
MG94_2[v-vshift][h-hshift] := synRate*observedFreq2__[transition2__][0];
}
else
{
MG94_1[h-hshift][v-vshift] := nonSynRate*observedFreq1__[transition__][0];
MG94_1[v-vshift][h-hshift] := nonSynRate*observedFreq1__[transition2__][0];
MG94_2[h-hshift][v-vshift] := nonSynRate*observedFreq2__[transition__][0];
MG94_2[v-vshift][h-hshift] := nonSynRate*observedFreq2__[transition2__][0];
}
}
}
}
/* the following function compute equil. codon frequencies */
function BuildCodonFrequencies (obsF)
{
PIStop = 1-obsF[3][0]*obsF[0][0]*obsF[2][0]-obsF[3][0]*obsF[2][0]*obsF[0][0]-obsF[3][0]*obsF[0][0]*obsF[0][0];
result = {61,1};
hshift = 0;
for (h=0; h<64; h=h+1)
{
if ((h==56)||(h==50)||(h==48))
{
hshift = hshift+1;
continue;
}
first = h$16;
second = h%16$4;
third = h%4;
result[h-hshift][0]=obsF[first][0]*obsF[second][0]*obsF[third][0]/PIStop;
}
return result;
}
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