input then the program will compute the fraction of nucleotides in both sequence

Question

input then the program will compute the fraction of nucleotides in both sequences that are shared. Consider the following example: Sequence 1: GCGTTAGCTAAAGCC Sequence 2: CCGTAAGCTATACCG The sequence identity ID1,2 between sequences 1 and 2 is calculated with the following equation: 1,2 where L is the length of the sequence, Ng s the nucleotide at position the function (A, B) equals l if A and B are the same nucleotide or 0 otherwise . A he example shown before, ID,1,2 0.73 since the two sequences share 11 identical nucleotides in t i E 1... L in sequence 1 For t same position and L = 15. Program Structure You program should do the following: 1. Ask the user to input sequences one amino acid at a time. To simplify the problem we will 2. The program should verify that the input nucleotides are only A, G, c,T,U. Otherwise it should retur that the sequence length must be L 10. The program should only accept or ask for 10 characters. an error and ask the user to input the right nucleotide

Explanation / Answer

Let's re-write the function (Niseq1, Niseq2), as (seq1, seq2, i), where length of seq1 = length of seq2 = L

This function (seq1, seq2, i) will return 1, if the characters at ith position in both the sequences, seq1 and seq2, are equal. Otherwise, it will return 0.

(i=1 to L)(seq1, seq2, i), means to check for each position in the sequences (from i=1 to i=L), and add up the results. Finally we divide the above result by length (L) of the sequences to get the sequence identity/match.

To implment the above formual, you need to use the following steps

1. initialize ID12 = 0.0
2. for i = 1 to 10
3.       If character at ith position in seq1 == character at ith position in seq2
4.              ID12 = ID12 + 1
5.       endIf
6. endfor
7. result = (ID12)/ L

Below is the working code of the requested program in JAVA

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import java.util.Scanner;

public class DNAMatch {

   /*
   * Function that finds out the sequence identity
   */
   public static double findSequenceIDentity(String seq1, String seq2, int L) {
       double iD12 = 0.0;
      
       for (int i=0; i<L; i++) {
           if (seq1.charAt(i) == seq2.charAt(i)) {
               iD12 += 1;
           }
       }
       return (iD12 / L);
   }
  
   /*
   * main method
   */
   public static void main(String args[]) {
       Scanner scanner = new Scanner(System.in);
       int L = 10;
      
       System.out.println("Enter Sequence-1, (one character at a time) : ");
       String seqOne = getInputSequence(scanner, L);
      
       System.out.println("Enter Sequence-2, (one character at a time) : ");
       String seqTwo = getInputSequence(scanner, L);
      
       System.out.println(" Sequence-1 is " + seqOne + " Sequence-2 is " + seqTwo);
       System.out.println("Sequence Identity of (1,2) is " + findSequenceIDentity(seqOne, seqTwo, L));
   }
  
   public static String getInputSequence(Scanner scanner, int L) {
       StringBuilder sequence = new StringBuilder();

       for (int i=1; i<=L; i++) {
           String character = scanner.next().trim().toUpperCase();
          
           /*
           * Read only if one character is entered
           * */
           if (character.length() == 1) {
               if (character.equals("A") || character.equals("G") ||
                       character.equals("C") || character.equals("T") || character.equals("U")) {
                   sequence.append(character);
               }
               else {
                   i--;
                   System.out.println("Invalid Character!");
               }
           }
           else {
               i--;
           }
       }
      
       return sequence.toString();
   }
  
  
}

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