Find start codon in a sequence - C programming

Question

[nathaydania]

Hi everyone,

I'm looking for some help to fix my program. I know it's not working, but I don't know how to make it work in C. If you could help me that would be awesome :)

//function that returns 1 if the codon is a start codon, or 0 if not.

int estStart(char seq[])
{
    int I = 0;

    if ((seq[i]=='A') & (seq[i+1]=='T') & (seq[i+2]=='G'))
    {
        return 1;
    }
    else
    {
        return 0;
    }
}

//function that returns 1 if the codon is a stop codon, or 0 if not.

int estStop(char seq[])
{
    int I = 0;

   ** if (((seq[i]=='T') & (seq[i+1]=='A') & (seq[i+2]=='A')) || ((seq[i]=='T') & (seq[i+1]=='A') & (seq[i+2]=='G')) || ((seq[i]=='T') & (seq[i+1]=='G') & (seq[i+2]=='A')))**
    {
        return 1;
    }
    else
    {
        return 0;
    }
}

//Function that returns index of the first start we can find, that is in the same phase as the stop codon.
int FindFisrtStart(char seq[], int start, int stop)
{
    int i, j, codon_start=0, codon_stop=0, found=0;

    for (j=start; j<stop; j++)
    {
        codon_stop = estStop([i, i+2]);

        if (codon_stop == 1)
        {
            for (i=start; i<stop; i++)
            {
                codon_start = estStart(seq[i,i+2]);

                if ((codon_start == 1) & (i%3 == j%3))
                {
                    found = i;
                    I = stop; //out of the 2nd "for"
                    j = stop; // out of the 1st "for"
                    return found; //we found what we needed
                }
            }
        }
    }

    if (trouve == 0)
    {
        return -1; //we didn't found
    }

}

First question:

Is there any way to make this line shorter:

if (((seq[i]=='T') & (seq[i+1]=='A') & (seq[i+2]=='A')) || ((seq[i]=='T') & (seq[i+1]=='A') & (seq[i+2]=='G')) || ((seq[i]=='T') & (seq[i+1]=='G') & (seq[i+2]=='A')))**

Second question:

I know this [i, i+2] doesn't work in C.

But how do you write it then? How do you get access to this characters inside the chain?

Third question:

Is there any other error you can see?

Thank you so much for your help!

Answer 1

[Pierre Lindenbaum]

use pointers

static int  estStop(const char* seq)
{
    return (strncmp(seq,"TAA",3)==0 || strncmp(seq,"ATG",3)==0 || ... ?1:0);
}

(...)

codon_stop = estStop(&seq[i]);

(...)