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1) how to concatenate DNA sequences as arguments and return the concatenated sequences
2) how to swap the contents of an array that has 6 elements at indexes 1 and 2.
3) biojava to reverse complmement a DNA strand and give it variable rev_com.
Expert Answer
package artifact1;
import org.biojava.nbio.core.exceptions.CompoundNotFoundException;
import org.biojava.nbio.core.sequence.DNASequence;
public class Main {
public static void main(String[] args) {
try {
DNASequence sequence1 = new DNASequence(“gtccttcttatcaaaacaacaccga”);
DNASequence sequence2 = new DNASequence(“gcaaagtcgagagggacttatccgc”);
System.out.println(“Sequence 1 : ” + sequence1.toString());
System.out.println(“Sequence 2 : ” + sequence2.toString());
// Concatenate DNA sequences
DNASequence combined = concatDNAsequences(sequence1, sequence2);
System.out.println(“Concatenated sequence is : ”
+ combined.toString());
// Swap elements of array
int array1[] = { 205, 306, 59, 89, 452, 10 };
System.out.println(“Before swap : “);
displayArray(array1);
int temp = array1[1];
array1[1] = array1[2];
array1[2] = temp;
System.out.println(“After swap : “);
displayArray(array1);
// Reverse complement DNA sequence
DNASequence rev_com = reverseComplement(sequence1);
System.out.println(“Reverse complemenet of sequence 1 is : ”
+ rev_com);
} catch (CompoundNotFoundException e) {
e.printStackTrace();
System.out.println(“Error !!!!”);
}
}
public static DNASequence concatDNAsequences(DNASequence seq1,
DNASequence seq2) {
StringBuffer sb = new StringBuffer(seq1.toString());
sb.append(seq2.toString());
try {
DNASequence result = new DNASequence(sb.toString());
return result;
} catch (CompoundNotFoundException e) {
e.printStackTrace();
return new DNASequence();
}
}
public static DNASequence reverseComplement(DNASequence seq) {
try {
return new DNASequence(seq.getReverseComplement()
.getSequenceAsString());
} catch (CompoundNotFoundException e) {
e.printStackTrace();
return new DNASequence();
}
}
public static void displayArray(int[] arr) {
for (int i = 0; i < arr.length; i++) {
System.out.print(arr[i]);
if (i != arr.length – 1) {
System.out.print(“,”);
}
}
System.out.println();
}
}
OUTPUT:
Sequence 1 : gtccttcttatcaaaacaacaccga
Sequence 2 : gcaaagtcgagagggacttatccgc
Concatenated sequence is : gtccttcttatcaaaacaacaccgagcaaagtcgagagggacttatccgc
Before swap :
205,306,59,89,452,10
After swap :
205,59,306,89,452,10
Reverse complemenet of sequence 1 is : tcggtgttgttttgataagaaggac
