Question

In C++

Write a function called findBestSimScore that takes a genome and a sequence and returns the highest similarity score found in the genome as a double.

Note: the term genome refers to the string that represents the complete set of genes in an organism, and sequence to refer to some substring or sub-sequence in the genome.

• Your function MUST be named findBestSimScore

• Your function should take two parameters in this order:

  • a string parameter for the genome (complete set of genes)

  • a string parameter for the sequence (sub-sequence of the genome)

• Your function should return the highest similarity score as a double.

• Your function should not print anything.

The best similarity scores is [0.0,1.0]

Our sequence is "ACT", which is a string of length 3. That means we need to compare our sequence with all the 3 character long sub-sequences (substrings) in the genome.

Examples:

genome sub-sequence	sequence	similarity score
ATACGC	ACT	0.33
ATACGC	ACT	0
ATACGC	ACT	0.66	← findBestMatch returns 0.66, since that is the highest similarity score found
ATACGC	ACT	0

Answer 1

NOTE: The complete program code is given to implement findBestSimScore() function. Please ignore the complete program code, if you want function code only.

Function Code to Copy:

double findBestSimScore(string genome, string seq)

{

    // Declare a variable count to find the number of

    // matching of a sequence.

    // Declare and initialize a variable max to 0 to

    // hold maximum number of a matching sequence.

    int count, max=0;

    // Check whether the length of genome is less than

    // sequence, then return 0.

    if(genome.length()<seq.length())

    {

        return 0;

    }

   

    // Use for loop to traverse through elements of

    // genome and sequence to find number of matchings.

    for(int i=0;i<genome.length()-seq.length()+1;i++)

    {

        // Initialize count variable to 0.

        count=0;

        // Inner for loop is used to compare all

        // character of sequence with same number of

        // genome string.

        for(int j=0;j<seq.length();j++)

        {

            // Check genome character is equal to sequence

            // character or not.

            if(genome[i+j]==seq[j])

                // Increment the count variable by 1.

                count++;

        }

        // Check if current count of matching is greater

        // than previous one.

        // Assign highest count value to max variable.

        if(count>max)

        {

            max=count;

        }

    }

    // Return a double type highest similarity score by

    // dividing max value with length of sequence string.

    return max/double(seq.length());

}

_________________________________________________________________________________

NOTE : PLEASE IGNORE COMPLETE PROGRAM CODE, IF YOU WANT FUNCTION CODE ONLY.

_________________________________________________________________________________

Complete Program Code to Copy:

// Include the required header files.

#include <iostream>

#include <string>

#include <iomanip>

#include <cmath>

using namespace std;

// Define a double type function findBestSimScore() to

// take genome and sequence as arguments and returns

// the highest similarity score.

double findBestSimScore(string genome, string seq)

{

    // Declare a variable count to find the number of

    // matching of a sequence.

    // Declare and initialize a variable max to 0 to

    // hold maximum number of a matching sequence.

    int count, max=0;

    // Check whether the length of genome is less than

    // sequence, then return 0.

    if(genome.length()<seq.length())

    {

        return 0;

    }

   

    // Use for loop to traverse through elements of

    // genome and sequence to find number of matchings.

    for(int i=0;i<genome.length()-seq.length()+1;i++)

    {

        // Initialize count variable to 0.

        count=0;

        // Inner for loop is used to compare all

        // character of sequence with same number of

        // genome string.

        for(int j=0;j<seq.length();j++)

        {

            // Check genome character is equal to sequence

            // character or not.

            if(genome[i+j]==seq[j])

                // Increment the count variable by 1.

                count++;

        }

        // Check if current count of matching is greater

        // than previous one.

        // Assign highest count value to max variable.

        if(count>max)

        {

            max=count;

        }

    }

    // Return a double type highest similarity score by

    // dividing max value with length of sequence string.

    return max/double(seq.length());

}

// Start the main() function

int main()

{

    // Declare two string type variable to hold genome

    // and sequence value.

    string genome, seq;

    // Declare variables to hold the highest similarity

    // score.

    double s, score;

    // Prompt the user to input genome string and sequence

    // string.

    cout<<"Enter a genome sub-sequence : ";

    getline(cin,genome);

    cout<<"Enter a sub-sequence to be searched : ";

    getline(cin,seq);

    // Call the findBestSimScore() function and store the

    // returned highest similarity score by function.

    s=findBestSimScore(genome,seq);

    // Store the highest similarity score without rounding

    // off the last digit.

    score=floor(100*s)/100;

    // Display the highest similarity score up to 2 decimal

    // points by using fixed and setprecision.

    cout<<"Highest similarity score : ";

    cout<<fixed<<setprecision(2)<<score<<endl;

    // Return 0 to the main() function.

    return 0;

// End of the main() function.

}