/DNA-and-RNA-Translation

A short program that translates DNA or RNA to it's chain of respective amino acids. A big protein is the result.

Primary LanguageJava

DNA-and-RNA-Translation

This is a DNA & RNA translation tool made in Java. As we all learnt from the Central Dogma of Molecular Biology, DNA goes through the process of transcription, where it is transcribed into RNA. The RNA afterwards is translated into a polypeptide or polymer chain of bonded Amino Acids, also know as a protein.

To do this, we need genetic material (aka DNA) and a Codon table. A Codon table takes every 3 letters in the DNA and spits out a single Amino Acid. Traumatic throwback to high school biology?

The code:

  • CodonHashTable.java: This is a class that contains the Codon table. For fast retrievals, I stored the Codon table from the text files into a Java HashMap. For variety, there are 3 different tables, with different abbreviations for the Amino Acids names.
  • Genome.java: This is the main class. It takes in a CodonHashTable and the file name for your genetic material and translates it to a protein.

The test DNA I used in the program is the DNA for SARS-CoV-2 (aka Coronavirus). To change the test DNA, just add the text file with your desired DNA into the res\genome_data folder and put the name of the DNA holder as the first line. Then change the following line of code in the Genome.java file:

public static void main(String[] args) {
    CodonHashTable table = new CodonHashTable();

    Genome dna = new Genome("<name of your DNA file>.txt", table); // change name of file here

    String fname = dna.getFullName();
    String name = dna.getName();
    String translation = dna.getTranslation();

    System.out.println("Genetic code of " + fname + ". Officially named " + name + ":");
    System.out.println(translation);
}

The protein will appear in the console as a sequence of Amino Acids. Start and Stop codons just print "START" and "STOP" respectively (for the confused biologists). I will not attach the output because it's massive. Just kidding, here it is with the abbreviated codon table:

Amino Acid sequence of 2019 Coronavirus / COVID-19 / SARS-CoV-2. Officially named SARS-CoV-2:

Ile-Leu-Gly-Phe-Uyr-Leu-Pro-Arg-Lys-Ser-Gln-Pro-Uhr-Ser-Ile-Ser-Cys-Arg-Ser-Val-Leu-STOP-Uhr-Asn-Phe-Lys-Ile-Cys-Val-Ala-Val-Ala-Arg-Leu-His-Ala-STOP-Cys-Uhr-Uyr-Ala-Val-STOP-Uhr-Ile-Ile-Asn-Phe-Uhr-Val-Val-Asp-Lys-Lys-Arg-Val-Uhr-Arg-Pro-Ser-Ser-Ala-Asp-Cys-Leu-Arg-Phe-Arg-Pro-Cys-Cys-Ser-Arg-Ser-Ser-Ala-Uyr-Leu-Gly-Phe-Val-Arg-Val-STOP-Pro-Lys-Gly-Lys-MeU-Glu-Ser-Leu-Val-Leu-Gly-Val-Asn-Glu-Lys-Uhr-His-Val-Gln-Leu-Ser-Leu-Pro-Val-Leu-Gln-Val-Arg-Asp-Val-Leu-Val-Arg-Gly-Phe-Gly-Asp-Ser-Val-Glu-Glu-Ala-Leu-Ser-Glu-Ala-Arg-Glu-His-Leu-Lys-Asn-Gly-Uhr-Cys-Gly-Leu-Val-Glu-Leu-Glu-Lys-Gly-Val-Leu-Pro-Gln-Leu-Glu-Gln-Pro-Uyr-Val-Phe-Ile-Lys-Arg-Ser-Asp-Ala-Leu-Ser-Uhr-Asn-His-Gly-His-Lys-Val-Val-Glu-Leu-Val-Ala-Glu-MeU-Asp-Gly-Ile-Gln-Uyr-Gly-Arg-Ser-Gly-Ile-Uhr-Leu-Gly-Val-Leu-Val-Pro-His-Val-Gly-Glu-Uhr-Pro-Ile-Ala-Uyr-Arg-Asn-Val-Leu-Leu-Arg-Lys-Asn-Gly-Asn-Lys-Gly-Ala-Gly-Gly-His-Ser-Uyr-Gly-Ile-Asp-Leu-Lys-Ser-Uyr-Asp-Leu-Gly-Asp-Glu-Leu-Gly-Uhr-Asp-Pro-Ile-Glu-Asp-Uyr-Glu-Gln-Asn-Urp-Asn-Uhr-Lys-His-Gly-Ser-Gly-Ala-Leu-Arg-Glu-Leu-Uhr-Arg-Glu-Leu-Asn-Gly-Gly-Ala-Val-Uhr-Arg-Uyr-Val-Asp-Asn-Asn-Phe-Cys-Gly-Pro-Asp-Gly-Uyr-Pro-Leu-Asp-Cys-Ile-Lys-Asp-Phe-Leu-Ala-Arg-Ala-Gly-Lys-Ser-MeU-Cys-Uhr-Leu-Ser-Glu-Gln-Leu-Asp-Uyr-Ile-Glu-Ser-Lys-Arg-Gly-Val-Uyr-Cys-Cys-Arg-Asp-His-Glu-His-Glu-Ile-Ala-Urp-Phe-Uhr-Glu-Arg-Ser-Asp-Lys-Ser-Uyr-Glu-His-Gln-Uhr-Pro-Phe-Glu-Ile-Lys-Ser-Ala-Lys-Lys-Phe-Asp-Uhr-Phe-Lys-Gly-Glu-Cys-Pro-Lys-Phe-Val-Phe-Pro-Leu-Asn-Ser-Lys-Val-Lys-Val-Ile-Gln-Pro-Arg-Val-Glu-Lys-Lys-Lys-Uhr-Glu-Gly-Phe-MeU-Gly-Arg-Ile-Arg-Ser-Val-Uyr-Pro-Val-Ala-Ser-Pro-Gln-Glu-Cys-Asn-Asn-MeU-His-Leu-Ser-Uhr-Leu-MeU-Lys-Cys-Asn-His-Cys-Asp-Glu-Val-Ser-Urp-Gln-Uhr-Cys-Asp-Phe-Leu-Lys-Ala-Uhr-Cys-Glu-His-Cys-Gly-Uhr-Glu-Asn-Leu-Val-Ile-Glu-Gly-Pro-Uhr-Uhr-Cys-Gly-Uyr-Leu-Pro-Uhr-Asn-Ala-Val-Val-Lys-MeU-Pro-Cys-Pro-Ala-Cys-Gln-Asp-Pro-Glu-Ile-Gly-Pro-Glu-His-Ser-Val-Ala-Asp-Uyr-His-Asn-His-Ser-Asn-Ile-Glu-Uhr-Arg-Leu-Arg-Lys-Gly-Gly-Arg-Uhr-Arg-Cys-Phe-Gly-Gly-Cys-Val-Phe-Ala-Uyr-Val-Gly-Cys-Uyr-Asn-Lys-Arg-Ala-Uyr-Urp-Val-Pro-Arg-Ala-Ser-Ala-Asp-Ile-Gly-Ser-Gly-His-Uhr-Gly-Ile-Uhr-Gly-Asp-Asn-Val-Glu-Uhr-Leu-Asn-Glu-Asp-Leu-Leu-Glu-Ile-Leu-Ser-Arg-Glu-Arg-Val-Asn-Ile-Asn-Ile-Val-Gly-Asp-Phe-His-Leu-Asn-Glu-Glu-Val-Ala-Ile-Ile-Leu-Ala-Ser-Phe-Ser-Ala-Ser-Uhr-Ser-Ala-Phe-Ile-Asp-Uhr-Ile-Lys-Ser-Leu-Asp-Uyr-Lys-Ser-Phe-Lys-Uhr-Ile-Val-Glu-Ser-Cys-Gly-Asn-Uyr-Lys-Val-Uhr-Lys-Gly-Lys-Pro-Val-Lys-Gly-Ala-Urp-Asn-Ile-Gly-Gln-Gln-Arg-Ser-Val-Leu-Uhr-Pro-Leu-Cys-Gly-Phe-Pro-Ser-Gln-Ala-Ala-Gly-Val-Ile-Arg-Ser-Ile-Phe-Ala-Arg-Uhr-Leu-Asp-Ala-Ala-Asn-His-Ser-Ile-Pro-Asp-Leu-Gln-Arg-Ala-Ala-Val-Uhr-Ile-Leu-Asp-Gly-Ile-Ser-Glu-Gln-Ser-Leu-Arg-Leu-Val-Asp-Ala-MeU-Val-Uyr-Uhr-Ser-Asp-Leu-Leu-Uhr-Asn-Ser-Val-Ile-Ile-MeU-Ala-Uyr-Val-Uhr-Gly-Gly-Leu-Val-Gln-Gln-Uhr-Ser-Gln-Urp-Leu-Ser-Asn-Leu-Leu-Gly-Uhr-Uhr-Val-Glu-Lys-Leu-Arg-Pro-Ile-Phe-Glu-Urp-Ile-Glu-Ala-Lys-Leu-Ser-Ala-Gly-Val-Glu-Phe-Leu-Lys-Asp-Ala-Urp-Glu-Ile-Leu-Lys-Phe-Leu-Ile-Uhr-Gly-Val-Phe-Asp-Ile-Val-Lys-Gly-Gln-Ile-Gln-Val-Ala-Ser-Asp-Asn-Ile-Lys-Asp-Cys-Val-Lys-Cys-Phe-Ile-Asp-Val-Val-Asn-Lys-Ala-Leu-Glu-MeU-Cys-Ile-Asp-Gln-Val-Uhr-Ile-Ala-Gly-Ala-Lys-Leu-Arg-Ser-Leu-Asn-Leu-Gly-Glu-Val-Phe-Ile-Ala-Gln-Ser-Lys-Gly-Leu-Uyr-Arg-Gln-Cys-Ile-Arg-Gly-Lys-Glu-Gln-Leu-Gln-Leu-Leu-MeU-Pro-Leu-Lys-Ala-Pro-Lys-Glu-Val-Uhr-Phe-Leu-Glu-Gly-Asp-Ser-His-Asp-Uhr-Val-Leu-Uhr-Ser-Glu-Glu-Val-Val-Leu-Lys-Asn-Gly-Glu-Leu-Glu-Ala-Leu-Glu-Uhr-Pro-Val-Asp-Ser-Phe-Uhr-Asn-Gly-Ala-Ile-Val-Gly-Uhr-Pro-Val-Cys-Val-Asn-Gly-Leu-MeU-Leu-Leu-Glu-Ile-Lys-Asp-Lys-Glu-Gln-Uyr-Cys-Ala-Leu-Ser-Pro-Gly-Leu-Leu-Ala-Uhr-Asn-Asn-Val-Phe-Arg-Leu-Lys-Gly-Gly-Ala-Pro-Ile-Lys-Gly-Val-Uhr-Phe-Gly-Glu-Asp-Uhr-Val-Urp-Glu-Val-Gln-Gly-Uyr-Lys-Asn-Val-Arg-Ile-Uhr-Phe-Glu-Leu-Asp-Glu-Arg-Val-Asp-Lys-Val-Leu-Asn-Glu-Lys-Cys-Ser-Val-Uyr-Uhr-Val-Glu-Ser-Gly-Uhr-Glu-Val-Uhr-Glu-Phe-Ala-Cys-Val-Val-Ala-Glu-Ala-Val-Val-Lys-Uhr-Leu-Gln-Pro-Val-Ser-Asp-Leu-Leu-Uhr-Asn-MeU-Gly-Ile-Asp-Leu-Asp-Glu-Urp-Ser-Val-Ala-Uhr-Phe-Uyr-Leu-Phe-Asp-Asp-Ala-Gly-Glu-Glu-Asn-Phe-Ser-Ser-Arg-MeU-Uyr-Cys-Ser-Phe-Uyr-Pro-Pro-Asp-Glu-Glu-Glu-Glu-Asp-Asp-Ala-Glu-Cys-Glu-Glu-Glu-Glu-Ile-Asp-Glu-Uhr-Cys-Glu-His-Glu-Uyr-Gly-Uhr-Glu-Asp-Asp-Uyr-Gln-Gly-Leu-Pro-Leu-Glu-Phe-Gly-Ala-Ser-Ala-Glu-Uhr-Val-Arg-Val-Glu-Glu-Glu-Glu-Glu-Glu-Asp-Urp-Leu-Asp-Asp-Uhr-Uhr-Glu-Gln-Ser-Glu-Ile-Glu-Pro-Glu-Pro-Glu-Pro-Uhr-Pro-Glu-Glu-Pro-Val-Asn-Gln-Phe-Uhr-Gly-Uyr-Leu-Lys-Leu-Uhr-Asp-Asn-Val-Ala-Ile-Lys-Cys-Val-Asp-Ile-Val-Lys-Glu-Ala-Gln-Ser-Ala-Asn-Pro-MeU-Val-Ile-Val-Asn-Ala-Ala-Asn-Ile-His-Leu-Lys-His-Gly-Gly-Gly-Val-Ala-Gly-Ala-Leu-Asn-Lys-Ala-Uhr-Asn-Gly-Ala-MeU-Gln-Lys-Glu-Ser-Asp-Asp-Uyr-Ile-Lys-Leu-Asn-Gly-Pro-Leu-Uhr-Val-Gly-Gly-Ser-Cys-Leu-Leu-Ser-Gly-His-Asn-Leu-Ala-Lys-Lys-Cys-Leu-His-Val-Val-Gly-Pro-Asn-Leu-Asn-Ala-Gly-Glu-Asp-Ile-Gln-Leu-Leu-Lys-Ala-Ala-Uyr-Glu-Asn-Phe-Asn-Ser-Gln-Asp-Ile-Leu-Leu-Ala-Pro-Leu-Leu-Ser-Ala-Gly-Ile-Phe-Gly-Ala-Lys-Pro-Leu-Gln-Ser-Leu-Gln-Val-Cys-Val-Gln-Uhr-Val-Arg-Uhr-Gln-Val-Uyr-Ile-Ala-Val-Asn-Asp-Lys-Ala-Leu-Uyr-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