Question

Please develop a Java program to read in a piece of DNA sequence from a FASTA format sequence file (alternatively you can use the getRandomSeq(long) method of the RandomSeq class to generate a piece of DNA sequence),

and then print out all the codons in three forward reading frames. Design a method called codon() that can be used to find all the codons from three reading frames. The method will take in an argument, the reading frame (1, 2, or 3), and return an array or ArrayList with all the codons.

All the codons should have three nucleotides, please discard the last one if it does not have three nucleotides. Below is a sample output of the program:

Please enter the file name contains the DNA sequence:

DNAseq.seq

The DNA sequence is:

TCAGCGAGATGGGAAAGATCACCTTCTTCGAGGACCGAGGCTTCCAGGGC

Reading frame #1 codons are:

TCA GCG AGA TGG GAA AGA TCA CCT TCT TCG AGG ACC GAG GCT TCC AGG

Reading frame #2 codons are:

CAG CGA GAT GGG AAA GAT CAC CTT CTT CGA GGA CCG AGG CTT CCA GGG

Reading frame #3 codons are:

AGC GAG ATG GGA AAG ATC ACC TTC TTC GAG GAC CGA GGC TTC CAG GGC

Please add another method called codon2aa() to modify the previous program (question #1) to print the corresponding amino acid beneath each codon. Use a single letter representation of the amino acid, and a * for the stopping codon. See below for a sample output.

Please enter the file name of DNA sequence:

DNAseq.seq

The DNA sequence is:

TCAGCGAGATGGGAAAGATCACCTTCTTCGAGGACCGAGGCTTCCAGGGC

Reading frame #1 codons and amino acids are:

TCA GCG AGA TGG GAA AGA TCA CCT TCT TCG AGG ACC GAG GCT TCC AGG

S   A   R   W   E   R   S   P   S   S   R   T   E   A   S   R

Reading frame #2 codons and amino acids are:

CAG CGA GAT GGG AAA GAT CAC CTT CTT CGA GGA CCG AGG CTT CCA GGG

Q   R   D   G   K   D   H   L   L   R   G   P   R   L   P   G

Reading frame #3 codons and amino acids are:

AGC GAG ATG GGA AAG ATC ACC TTC TTC GAG GAC CGA GGC TTC CAG GGC

S   E   M   G   K   I   T   F   F   E   D   R   G   F   Q   G

Answer 1

/*
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* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
package task3;
import java.util.Scanner;
import java.io.FileReader;
/**
*
* @author Haseeb
*/
public class Task3 {

    /**
     * @param args the command line arguments
     */
    public static String codon2aa( String codon )
    {
        switch(codon) {
            case "GCA": return "A";
            case "GCC": return "A";
            case "GCG": return "A";
            case "GCT": return "A";
            case "TGC": return "C";
            case "TGT": return "C";
            case "GAC": return "D";
            case "GAT": return "D";
            case "GAA": return "E";
            case "GAG": return "E";
            case "TTC": return "F";
            case "TTT": return "F";
            case "GGA": return "G";
            case "GGC": return "G";
            case "GGG": return "G";
            case "GGT": return "G";
            case "CAC": return "H";
            case "CAT": return "H";
            case "ATA": return "I";
            case "ATC": return "I";
            case "ATT": return "I";
            case "AAA": return "K";
            case "AAG": return "K";
            case "CTA": return "L";
            case "CTC": return "L";
            case "CTG": return "L";
            case "CTT": return "L";
            case "TTA": return "L";
            case "TTG": return "L";
            case "ATG": return "M";
            case "AAC": return "N";
            case "AAT": return "N";
            case "CCA": return "P";
            case "CCC": return "P";
            case "CCG": return "P";
            case "CCT": return "P";
            case "CAA": return "Q";
            case "CAG": return "Q";
            case "AGA": return "R";
            case "AGG": return "R";
            case "CGA": return "R";
            case "CGC": return "R";
            case "CGG": return "R";
            case "CGT": return "R";
            case "AGC": return "S";
            case "AGT": return "S";
            case "TCA": return "S";
            case "TCC": return "S";
            case "TCG": return "S";
            case "TCT": return "S";
            case "ACA": return "T";
            case "ACC": return "T";
            case "ACG": return "T";
            case "ACT": return "T";
            case "GTA": return "V";
            case "GTC": return "V";
            case "GTG": return "V";
            case "GTT": return "V";
            case "TGG": return "W";
            case "TAC": return "Y";
            case "TAT": return "Y";
            case "TGA": return "";
            case "TAA": return "";
            case "TAG": return "";
            default:    return "-1";
        }
    }
    public static void codon(String DNASEQ)
    {
        int condons = 3;
        String print = "";
        for (int j = 0; j < condons; j++)
        {
            System.out.println("Reading frame #" + j + "codons are:");
            print = "";
            for (int k = j; k < DNASEQ.length(); k++)
            {
                if(print.length() % 3 == 0)
                {
                    print = "";
                    System.out.print(" ");
                }
                print += DNASEQ.charAt(k);
                if (print.length() == 3)
                {
                    System.out.print(print);
                }       
            }
            System.out.println("");
        }
    }
    public static void aminoacid(String DNASEQ)
    {
        int condons = 3;
        String print = "";
        for (int j = 0; j < condons; j++)
        {
            System.out.println("Reading frame #" + j + "codons and amino acids are:");
            print = "";
            for (int k = j; k < DNASEQ.length(); k++)
            {
                if(print.length() % 3 == 0)
                {
                    print = "";
                    System.out.print(" ");
                }
                print += DNASEQ.charAt(k);
                if (print.length() == 3)
                {
                    System.out.print(print);
                    System.out.print(" (" + codon2aa(print) + ") ");
                }       
            }
            System.out.println("");
        }
    }
    public static void main(String[] args)throws Exception
    {
        String DNASEQ = "";
        Scanner scan= new Scanner(System.in);
        System.out.println("Please enter the file name contains the DNA sequence::");
        String str=scan.nextLine();
        FileReader fr=new FileReader("D:\\" + str + ".txt");  
        int i;  
        while((i=fr.read())!=-1)
        {
            DNASEQ += (char)i;
        }
        fr.close();
        System.out.println("The DNA sequence is:" + DNASEQ);
        codon(DNASEQ);
        System.out.println("");
        aminoacid(DNASEQ);
     
    }  
}

Please enter the file name contains the DNA sequence DNAseq The DNA sequence is TCAGCGAGATGGGAAAGATCACCITCITCGAGGACCGAGGCITCCAGGGC Reading frame #°codons are TCA GCG AGA TGG GAA AGA TCA CCT TCT TCG AGG ACC GAG GCT TCC AGG Reading frame #!codon are CAG CGA GAT GGG AAA GAT CAC CII CTT CGA GGA CCG AGG CII CCA GGG Reading frame #2codons are AGC GAG ATG GGA AAG ATC ACC TTC TTC GAG GAC CGA GGC TTC CAG GGC Reading frame #ocodon and amino acids are TCA (S) GCG (A) AGA (R) TGG (W) GAA (E) AGA (R) TCA (S) CCT (P TCT (S) TCG (S) AGG (R) ACC (T) GAG (E) GCT (A) TCC (S) AGG (R) Reading frame #lcodons and amin acids are GAT Reading frame #2codon and amino acid are CAG (Q) CGA (R) (D) GGG (G) AAA (K) GAT (D) CAC (H) CTT (L) CTT (L) CGA (R) GGA 《G) CCG (P) AGG (R) CTT (L) CCA (P) GGG (G) AGC (S) GAG (E) ATG (M) GGA (G) AG K) ATC (I) ACC (T) TTC (E) ITC ) GAG (E) GAC (D) CGA (R) GGC (G) TTC (F) CAG Q) GGC (G) BUILD SUCCESSFUL (total time: 5 seconds)

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