I've got some Java code that runs quite the expected way, but it's taking some amount of time -some seconds- even if the job is just looping through an array.

The input file is a Fasta file as shown in the image below. The file I'm using is 2.9Mo, and there are some other Fasta file that can take up to 20Mo.

And in the code im trying to loop through it by bunches of threes, e.g: AGC TTT TCA ... etc The code has no functional sens for now but what I want is to append each Amino Acid to it's equivalent bunch of Bases. Example :

AGC - Ser / CUG Leu / ... etc

So what's wrong with the code ? and Is there any way to do it better ? Any optimization ? Looping through the whole String is taking some time, maybe just seconds, but need to find a better way to do it.

import java.io.BufferedReader;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileReader;
import java.io.IOException;

public class fasta {
    public static void main(String[] args) throws IOException {

        File fastaFile;
        FileReader fastaReader;
        BufferedReader fastaBuffer = null;
        StringBuilder fastaString = new StringBuilder();

        try {
            fastaFile = new File("res/NC_017108.fna");
            fastaReader = new FileReader(fastaFile);
            fastaBuffer = new BufferedReader(fastaReader);
            String fastaDescription = fastaBuffer.readLine();
            String line = fastaBuffer.readLine();

            while (line != null) {
                fastaString.append(line);
                line = fastaBuffer.readLine();
            }

            System.out.println(fastaDescription);
            System.out.println();
            String currentFastaAcid;

            for (int i = 0; i < fastaString.length(); i+=3) {
                currentFastaAcid = fastaString.toString().substring(i, i + 3);
                System.out.println(currentFastaAcid);
            }

        } catch (NullPointerException e) {
            System.out.println(e.getMessage());
        } catch (FileNotFoundException e) {
            System.out.println(e.getMessage());
        } catch (IOException e) {
            System.out.println(e.getMessage());
        } finally {
            fastaBuffer.close();
        }

    }

}