Gene Finding via GC content

Problem

  • Within a long region of genomic sequence, genes are often characterised by having a higher GC-content in contrast to the background GC-content for the entire genome.
  • Write a program to prompt the user for a string of DNA bases (ACTG)
  • Calculate the ratio of G’s and C’s
  • If the ratio is > .60, report that the sequence is likely a gene, otherwise report it is probably not.

A contextually-similar problem is Gene Finding via TATA box search.

Solution

/*
Test Case 1:
Input: A (this is an example of a string with no Gs or Cs)
Expected Output: 0, not a gene
Actual Output: 0, not a gene
 
Test Case 2:
Input: G (this is an example of a string with only Gs and Cs)
Expected Output: 1, probably a gene
Actual Output: 1, probably a gene
 
Test Case 3:
Input: ACATAGACTAG (this is an example of a string with a mix of all four bases)
Expected Output: .36, probably not a gene
Actual Output: .36, probably not a gene
*/
 
#include <iostream>
#include <string>
 
using namespace std;
 
int main()
{
	// Inputs: DNA sequence
	// Outputs ratio of G&C to total, and prediction of whether or not it's a gene
 
	// Prompt the user
	cout << "Please input a DNA sequence: ";
	string dna_string;
	cin >> dna_string;
 
	int gc_count = 0;
	// Calculate GC-content
	for (int i = 0; i < dna_string.length(); i++)
	{
		// Count the number of Gs and Cs
		string base_at_i = dna_string.substr(i, 1);
 
		// The following statement can be uncommented to check that our loop is working correctly.
		// cout << "base at i is " << base_at_i << endl;
 
		if (base_at_i == "G" || base_at_i == "C")
		{
			gc_count++;
		}
	}
 
	cout << "Total GC count was " << gc_count << endl;
 
	// Divide by total string length to get ratio, making sure to account for integer division problems.
	double gc_ratio = 1.0 * gc_count / dna_string.length();
	cout << "GC ratio for sequence was " << gc_ratio << endl;
 
	// if ratio > .60, then report it's a gene
	if (gc_ratio > .6)
	{
		cout << "You've got a gene on your hands!" << endl;
	}
	else
	{
		cout << "Probably not a gene..." << endl;
	}
 
	system("pause");
	return 0;
}
cs-142/gene-finding-via-gc-content.txt · Last modified: 2015/05/12 18:26 by cs142ta
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