Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Tutorials
Tools
Jobs
Forum
Planet
All »
Home
Log In
Question: GC content by c programming
0
gravatar for banerjeesourya1
6 weeks ago by
banerjeesourya1 • 0
banerjeesourya1 • 0 wrote:

how to find GC content in a given DNA sequence by c programming ? Not in any other language.
C gene genome • 174 views
ADD COMMENT • link •
modified 6 weeks ago by Alex Reynolds ♦ 31k • written 6 weeks ago by banerjeesourya1 • 0
0
gravatar for Alex Reynolds
6 weeks ago by
Alex Reynolds ♦ 31k
Seattle, WA USA
Alex Reynolds ♦ 31k wrote:

One way is to read DNA sequence into a char [] or terminated char * and loop over each character:

#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <ctype.h>

int
main(int argc, const char** argv)
{
    unsigned int gc = 0;
    const char * sequence = "gtcctttTctaGacAtaNNaggtgggaCat";
    size_t sequence_len = strlen(sequence);

    for (size_t i = 0; i < sequence_len; i++) {
        char residue = (char) toupper(sequence[i]);
        switch (residue) {
            case 'C':
            case 'G':
                gc++;
                break;
            case 'A':
            case 'T':
            case 'N':
            default:
                break;
        }
    }

    fprintf(stdout, "GC content: %f\n", (float) gc / sequence_len);

    return EXIT_SUCCESS;
}

Multiply the fraction by 100 to get a percentage.
ADD COMMENT • link modified 6 weeks ago • written 6 weeks ago by Alex Reynolds ♦ 31k
Please log in to add an answer.

Similar posts • Search »

Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 932 users visited in the last hour