Hi everyone,

I'm learning bioinformatics and I need some help with a program in C.

The program is aimed at calculating a Khi 2 for a sequence, to make a comparison between the percentage of GC observed and the percentage of GC expected.

Here are the functions I've made:

//to count how many G or C there are in the sequence

int countGCtotal(char seq[], int lg)
{
    int I = 0;
    int count_GCtotal = 0;

    do
    {
        if ((seq[i]=='G') || (seq[i]=='C'))
        {
            count_GCtotal += 1;
        }

        i++;

    }while(i<lg);

    return (count_GCtotal);
}

//to count G and C with a step of 3 nucleotides

int countGC3by3(char seq[], int lgSeq)
{
    int i, compteur_GC3en3=0;

    for(i=2; i<lgSeq; i+=3) /*phase 1*/
   {
       if ((seq[i]=='G') || (seq[i]=='C'))
            {
                count_GC3by3 +=1;
            }
    }

    return count_GC3by3;
}

// to calculate the Khi 2

float calcKhi2(char seq[], int lg)
{
    float khi2Calc=0.0, GC=0.0;
    int numberGC3by3=0, numberGCtotal=0;

    numberGC3by3 = countGC3by3(seq, lg);
    numberGCtotal = countGCtotal(seq, lg);
    GC=(float)numberGCtotal/3;

    khi2Calc = (float) (pow((float) numberGC3by3-GC,2)/GC);

}

So the Khi2 is calculated for the first position (phase 1).

My problem is: how to calculate the Khi 2 including phases 2 and 3?

How to calculate the number of GC 3 by 3 in phase 2 and 3 (using the function countGC3by3 - without changing this function)?

Thanks a lot for your help ! :)