How do I use a non standard translation table?

The convenient translate() method in RNATools, used in the general translation example, is only useful if you want to use the “Universal” translation table. This is not so good if you want to use one of those weird Mitochondrial translation tables. Fortunately this can be done in BioJava. RNATools also has a static method getGeneticCode(String name) that lets you get a TranslationTable by name.

The following TranslationTables are available:

• FLATWORM_MITOCHONDRIAL
• YEAST_MITOCHONDRIAL
• ASCIDIAN_MITOCHONDRIAL
• EUPLOTID_NUCLEAR
• UNIVERSAL
• INVERTEBRATE_MITOCHONDRIAL
• BLEPHARISMA_MACRONUCLEAR
• ALTERNATIVE_YEAST_NUCLEAR
• BACTERIAL
• VERTEBRATE_MITOCHONDRIAL
• CILIATE_NUCLEAR
• MOLD_MITOCHONDRIAL
• ECHINODERM_MITOCHONDRIAL

These are also the valid names that can be used as an argument in the static RNATools.getGeneticCode(String name) method. These names are also available as static Strings in the TranslationTools class.

The following program shows the use of the Euplotid Nuclear translation table (where UGA = Cys).

```java import org.biojava.bio.seq.*; import org.biojava.bio.symbol.*;

public class AlternateTranslation {

 public static void main(String[] args) {

   //get the Euplotoid translation table
   TranslationTable eup = RNATools.getGeneticCode(TranslationTable.EUPL_NUC);

   try {
     //make a DNA sequence including the 'tga' codon
     SymbolList seq = DNATools.createDNA("atgggcccatgaaaaggcttggagtaa");

     //transcribe to RNA
     seq = RNATools.transcribe(seq);

     //view the RNA sequence as codons, this is done internally by RNATool.translate()
     seq = SymbolListViews.windowedSymbolList(seq, 3);

     //translate
     SymbolList protein = SymbolListViews.translate(seq, eup);

     //print out the protein
     System.out.println(protein.seqString());
   }
   catch (Exception ex) {
     ex.printStackTrace();
   }
 }

} ```