Introduction Genomics DNA is the fundamental encoding of the

Introduction Genomics DNA is the fundamental encoding of the instructions that govern the operation of living cells and by extension, biological organisms. You can think of DNA as a storage medium in which the pro- gram that executes within all of your cells is written. The \"machine code\" of DNA, corresponding to the byte-code of Java, consists of only four nucleotides: four amino acids that are arranged in a linear sequence along the DNA molecule. These four bases are: guanine (G, adenine (A), thymine (T), and cytosine (C). So, a DNA molecule can be represented as a string made up of those four letters. The science of bioinformatics is largely concerned with computations on such genetic strings, or sequences. There are a variety of computations that one might perform on genetic sequences. We will investigate two types: basic statistics of individual sequences and pairwise alignments used to compare pairs of sequences.

Solution

import java.util.*;
public class DNAsequence {
   static Scanner sc=new Scanner(System.in);
static   int countc=0;
static   int countg=0;
static float fraction=0.0f;
   public static void main(String[] args) {
       boolean valid;
       String DNA;
       String DNA2;
  
       while(true)
       {
       System.out.println(\"Enter DNA Sequence: \");
       DNA = sc.nextLine();
       if(chkvalid(DNA))
       {   
       System.out.println(\"Sequence 1: \" + DNA);
       countss(DNA);
       countgg(DNA);
       detfraction(DNA);
       System.out.print(\"Complement: \");   
       complement(DNA);
       break;
       }
       else
       {
       System.out.println(\"Please enter Valid DNA Sequence!\");   
       }
         
             
         
       }      
       while(true)
       {
       System.out.println(\"Enter DNA2 Sequence: \");
       DNA2 = sc.nextLine();
       if(chkvalid(DNA2))
       {   
       System.out.println(\"Sequence 1: \" + DNA2);
       countss(DNA2);
       countgg(DNA2);
       detfraction(DNA2);
       System.out.print(\"Complement: \");   
       complement(DNA2);
       break;
       }
       else
       {
       System.out.println(\"Please enter Valid DNA Sequence!\");   
       }
         
             
         
       }      
      
       bestalignment(DNA,DNA2);
   }
   private static boolean chkvalid(String DNA) {
       if (DNA.matches(\"[ATGC]+\")) {
           return true;
       }else
           return false;
      
   }
   public static void countss(String DNA){
       for(int i=0;i<DNA.length();i++){
           if(DNA.charAt(i)==\'C\')
               countc++;
      
       }
       System.out.println(\"count of c:\"+countc);
  
   }
   public static void countgg(String DNA){
       for(int i=0;i<DNA.length();i++){
           if(DNA.charAt(i)==\'G\')
               countg++;
   }
       System.out.println(\"count of g:\"+countg);
      
   }
   public static void detfraction(String DNA){
       if(countc >=DNA.length()/2||countg>=DNA.length()/2)
           fraction=0.5f;
           System.out.println(\"cg ratio:\"+fraction);
   }
   public static void complement(String DNA){
       String cp=\"\";
       for(int i=0;i<DNA.length();i++){
           if(DNA.charAt(i)==\'A\')
               cp+=\'T\';
           else if(DNA.charAt(i)==\'T\')
               cp+=\'A\';
           if(DNA.charAt(i)==\'C\')
               cp+=\'G\';
           else if(DNA.charAt(i)==\'G\')
               cp+=\'C\';
          
              
       }
       System.out.println(cp);
   }
   public static void bestalignment(String DNA,String DNA2){
       List<Integer>alist=new ArrayList<Integer>();
       int bigs=0;
       int add=0;
       int s1=DNA.length();
       int s2=DNA2.length();
       int diff1=0;
       int diff2=0;
       if(s1>s2)
       diff1=s1-s2;
       else
           diff1=s2-s1;
       diff2=diff1;
       int i=0;
       while(i<=diff2){
           for(int j=0;j<DNA2.length();j++){
               char a=DNA.charAt(j+i);
               char b=DNA2.charAt(j);
               if(a==b)
                   add++;
              
           }
           alist.add(add);
           add=0;
       i++;
      
   }
       //System.out.println(alist);
       for(int k=0;k<alist.size();k++){
           if(alist.get(k)>bigs)
               bigs=alist.get(k);
       }
       System.out.println(\"best alignment is:\"+bigs);
          
   }
}

OUTPUT:
Enter DNA Sequence:
AATCTATA
Sequence 1: AATCTATA
count of c:1
count of g:0
cg ratio:0.0
Complement: TTAGATAT
Enter DNA2 Sequence:
AAGATA
Sequence 1: AAGATA
count of c:1
count of g:1
cg ratio:0.0
Complement: TTCTAT
[4, 1, 3]
best alignment is:4


OUTPUT:
Enter DNA Sequence:
CTAAGT
Sequence 1: CTAAGT
count of c:1
count of g:1
cg ratio:0.0
Complement: GATTCA
Enter DNA2 Sequence:
GT
Sequence 1: GT
count of c:1
count of g:2
cg ratio:0.5
Complement: CA
best alignment is:2