Question

I have written the below code for LCS. It works for many cases but breaks for the one below. I do not understand where my code is breaking. Please help. The code is in C#

namespace LongestCommonSubsequenceBF
{
class Program
{
    static void Main(string[] args)
    {

        string B = "AAACCGTGAGTTATTCGTTCTAGAA";
        string A = "CACCCCTAAGGTACCTTTGGTTC";
        //find LCS in A,B starting from index 0 of each
        int longestCommonSubsequence = LCS(A, B, 0, 0);
        Console.WriteLine(longestCommonSubsequence);
        Console.Read();

    }

    //Find the longest common subsequnce starting from index1 in A and index2 in B
    //Pass A as shorter string
    public static int LCS(String A, String B, int index1, int index2)
    {
        int max = 0;
        if (index1 == A.Length)
        {
            //You have reached beyond A and thus no subsequence
            return 0;
        }
        if (index2 == B.Length)
        {   //you may reach end of 2nd string. LCS from that end is 0
            return 0;
        }

        for (int i = index1; i < A.Length ; i++)
        {
            int exist = B.IndexOf(A[i],index2);
            if (exist != -1)
            {
             //   found = true;

                int temp = 1 + LCS(A, B, i + 1, exist + 1);
                if (max < temp)
                {
                    max = temp;
                }


            }


        }
        return max;

    }
  }
}

Answer 1

Why do you think your algorithm is broken? The longest common subsequence is ACCTAGTATTGTTC, which is 14 characters long:

string B = "AAACCGTGAGTTATTCGTTCTAGAA";
              ^^^ ^ ^^ ^^^^ ^^^^

string A = "CACCCCTAAGGTACCTTTGGTTC";
             ^^^  ^ ^^ ^^  ^^ ^ ^^^

(I modified your algorithm to return the sequence instead of just the length.)