How do I translate a DNA or RNA Sequence or SymbolList to Protein?

To translate a DNA sequence you need to do the following

  • Transcribe to RNA.
  • Get a triplet (codon) view on the SymbolList.
  • Translate to protein.

Almost all of this can be achieved using static methods from BioJava tools classes. The following block of code demonstrates the procedure. Obviously if you already have an RNA sequence there is no need to transcribe it.

NOTE: if you try and create a ‘triplet view’ on a SymbolList or Sequence who’s length is not evenly divisible by three an IllegalArgumentException will be thrown. See ‘how to get a subsequence’ for a description of how to get a portion of a Sequence for translation.

```java import*; import*;

public class Translate {

 public static void main(String[] args) {
   try {
     //create a DNA SymbolList
     SymbolList symL = DNATools.createDNA("atggccattgaatga");

     //transcribe to RNA (after biojava 1.4 this method is deprecated)
     symL = RNATools.transcribe(symL);

     //transcribe to RNA (after biojava 1.4 use this method instead)
     symL = DNATools.toRNA(symL);
     //translate to protein
     symL = RNATools.translate(symL);

     //prove that it worked
    }catch (IllegalAlphabetException ex) {
      * this will occur if you try and transcribe a non DNA sequence or translate
      * a sequence that isn't a triplet view on a RNA sequence.
    }catch (IllegalSymbolException ex) {
     // this will happen if non IUB characters are used to create the DNA SymbolList

} ```