BioJava:Cookbook:Translation:Single

From BioJava

How do I translate a single codon to a single amino acid?

The general translation example shows how to use RNATools to translate a RNA SymbolList into a Protein SymbolList but most of what goes on is hidden behind the convenience method translate(). If you only want to translate a single codon into a single amino acid you get exposed to a bit more of the gory detail but you also get a chance to figure out more of what is going on under the hood.

There are actually a number of ways to do this, below I have presented only one.

import org.biojava.bio.seq.*;
import org.biojava.bio.symbol.*;
 
public class SingleTranslationDemo {
  public static void main(String[] args) {
    //make a compound alphabet where codons are Symbols
    Alphabet a = AlphabetManager.alphabetForName("(RNA x RNA x RNA)");
 
    //get our translation table using one of the static names from TranslationTable
    TranslationTable table = RNATools.getGeneticCode(TranslationTable.UNIVERSAL);
 
    try {
      //make a 'codon'
      SymbolList codon = RNATools.createRNA("UUG");
 
 
      //get the representation of that codon as a Symbol
      Symbol sym = a.getSymbol(codon.toList());
 
      //translate to amino acid
      Symbol aminoAcid = table.translate(sym);
 
      /*
       * This bit is not required for the translation it just proves that the
       * Symbol is from the right Alphabet. An Exception will be thrown if it
       * isn't.
       */
      ProteinTools.getTAlphabet().validate(aminoAcid);
 
      //i think it is Leucine
      System.out.println(aminoAcid.getName());
 
    }
    catch (IllegalSymbolException ex) {
      ex.printStackTrace();
    }
  }
}