Answer:
See explaination
Explanation:
import java.util.*;
class Dna
{
public static void main(String args[])
{
Scanner sc = new Scanner(System.in);
boolean b = false; //boolean variable to check validity
String s1="",s2="";
//input 1st sequence from user
while(b != true)
{
System.out.print("Sequence 1: ");
s1 = sc.nextLine();
b = isValid(s1); //checks validity
}
int c = findCount(s1); //finds C-Count for 1st sequence
double ratio = findRatio(c, s1); //finds CG-Ratio for 1st sequence
String complement = findComplement(s1); //finds complement of 1st sequence
System.out.println("C-count: "+c);
System.out.println("CG-ratio: "+ratio);
System.out.println("Complement: "+complement+"\n");
b = false; //re-initialize for 2nd sequence
//input 2nd sequence from user
while(b != true)
{
System.out.print("Sequence 2: ");
s2 = sc.nextLine();
b = isValid(s2); //checks validity
}
c = findCount(s2); //finds C-Count for 2nd sequence
ratio = findRatio(c, s2); //finds CG-Ratio for 2nd sequence
complement = findComplement(s2); //finds complement of 2nd sequence
System.out.println("C-count: "+c);
System.out.println("CG-ratio: "+ratio);
System.out.println("Complement: "+complement+"\n");
findAlignment(s1, s2); //finds best alignment score
}
/* This function determines validity of a sequence */
public static boolean isValid(String s)
{
boolean b = true;
for(int i=0; i<s.length(); i++)
{
char c = s.charAt(i);
if(!(c=='A' || c=='C' || c=='G' || c=='T'))
{
b = false;
break;
}
}
return b;
}
/* This function finds count of 'C' by iterating over string */
public static int findCount(String s)
{
int count = 0;
for(int i=0; i<s.length(); i++)
{
if(s.charAt(i) == 'C')
count++;
}
return count;
}
/**
This function finds CG-Ratio by iterating over string
and finding count of 'C' and 'G' and dividing the count by
size of string
*/
public static double findRatio(int c, String s)
{
int count = 0;
int length = s.length();
for(int i=0; i<length; i++)
{
if(s.charAt(i) == 'C' || s.charAt(i) == 'G')
count++;
}
double ratio = (double)count/length;
ratio = (double) Math.round(ratio * 1000) / 1000;
return ratio;
}
/* This function finds complement of a sequence */
public static String findComplement(String s)
{
String sc = "";
for(int i=0; i<s.length(); i++)
{
char c = s.charAt(i);
if(c == 'A')
sc = sc + "T";
else if(c == 'T')
sc = sc + "A";
else if(c == 'C')
sc = sc + "G";
else if(c == 'G')
sc = sc + "C";
}
return sc;
}
/**
This function finds maximum Alignment score by shifting
the string with lower size by 1 until the difference
between the size of both strings and calculating count
of characters match
*/
public static void findAlignment(String s1, String s2)
{
int offset = 0; //highest shift upto which 2nd sequence need to be shifted
int maxOffset = 0; //the offset where we get maximum alignment score
int maxAllignment = 0; //stores max Alignment score
int l1 = s1.length(); //length of 1st sequence
int l2 = s2.length(); //length of 2nd sequence
int min = 0; //stores the length of sequence with smaller size
//calculate difference between size of both sequences
//to determine offset
if(l1>l2)
{
offset = l1 - l2;
min = l2;
}
else if(l1<l2)
{
offset = l2 - l1;
min = l1;
}
else
{
offset = 1; //ensures single iteration for equi-length sequences
min = l1;
}
//loop to find max alignment score
for(int i=0; i<offset; i++)
{
int count = 0; //counts alignment score for each offset
//This loop checks the count for each alignment
for(int j=0; j<min; j++)
{
if(s1.charAt(j+i) == s2.charAt(j))
count++;
}
//store highest alignment score in maxAlignment
//and shift of the smaller sequence in maxOffset
if(count > maxAllignment)
{
maxAllignment = count;
maxOffset = i;
}
}
//Print the alignment score and alignment of sequences
if(l1>l2)
{
System.out.println("Best alignment score: "+maxAllignment);
System.out.println(s1);
for(int i=0; i<maxOffset; i++)
System.out.print(" ");
System.out.println(s2);
}
else if(l2>l1)
{
System.out.println("Best alignment score: "+maxAllignment);
for(int i=0; i<maxOffset; i++)
System.out.print(" ");
System.out.println(s1);
System.out.println(s2);
}
else
{
System.out.println("Best alignment score: "+maxAllignment);
System.out.println(s1);
System.out.println(s2);
}
}
}
