BioJava:Cookbook:Translation:SixFrames

From BioJava

How can I translate all six frames of a nucleotide Sequence?

This is probably one of the more frequent tasks in bioinformatics and one of the most frequent questions posted to the mailing list.

Six frame translations are good for identifying large ORFs which can be indicators of coding regions, at least in species that don't have introns. A six frame translation is a simple matter of taking subsequences of the sequence(s) of interest and reverse complementing/translating as appropriate. The only trick is figuring out how to take the subsequences so you have regions that are equally divisible by three

The following example shows a simple program that will six frame translate all sequences in a file and print the results to STDOUT in fasta format.

import java.io.BufferedReader;
import java.io.FileReader;
 
import org.biojava.bio.Annotation;
import org.biojava.bio.seq.DNATools;
import org.biojava.bio.seq.RNATools;
import org.biojava.bio.seq.Sequence;
import org.biojava.bio.seq.SequenceIterator;
import org.biojava.bio.seq.SequenceTools;
import org.biojava.bio.seq.io.SeqIOTools;
import org.biojava.bio.symbol.SymbolList;
 
/**
 * <p>Program to six-frame translate a nucleotide sequence</p>
 */
 
public class Hex {
  /**
   * Call this to get usage info, program terminates after call.
   */
  public static void help() {
    System.out.println(
        "usage: java Hex <file> <format eg fasta> <dna|rna>");
    System.exit( -1);
  }
 
  public static void main(String[] args) throws Exception{
    if (args.length != 3) {
      help();
    }
 
    BufferedReader br = null;
    
    //file format (eg fasta)
    String format = args[1];
    
    //sequence type (eg dna)
    String alpha = args[2];
 
    try {
      br = new BufferedReader(new FileReader(args[0]));
 
      SequenceIterator seqi =
          (SequenceIterator)SeqIOTools.fileToBiojava(format, alpha, br);
 
      //for each sequence
      while(seqi.hasNext()){
        Sequence seq = seqi.nextSequence();
 
        //for each frame
        for (int i = 0; i < 3; i++) {
          SymbolList prot;
          Sequence trans;
 
          //take the reading frame
          SymbolList syms = seq.subList(
                i+1,
                seq.length() - (seq.length() - i)%3);
 
 
          //if it is DNA transcribe it to RNA
          if(syms.getAlphabet() == DNATools.getDNA()){
            //before BJ1.4 use this method
	    syms = RNATools.transcribe(syms);
	    //after BJ1.4 use this method
	    syms = DNATools.toRNA(syms);
          }
 
          //output forward translation to STDOUT
          prot = RNATools.translate(syms);
          trans = SequenceTools.createSequence(prot, "",
                                               seq.getName()+
                                               "TranslationFrame: +"+i,
                                               Annotation.EMPTY_ANNOTATION);
          SeqIOTools.writeFasta(System.out, trans);
 
          //output reverse frame translation to STDOUT
          syms = RNATools.reverseComplement(syms);
          prot = RNATools.translate(syms);
          trans = SequenceTools.createSequence(prot, "",
                                               seq.getName() +
                                               " TranslationFrame: -" + i,
                                               Annotation.EMPTY_ANNOTATION);
          SeqIOTools.writeFasta(System.out, trans);
        }
      }
    }
    finally {
      //tidy up
      if(br != null){
        br.close();
      }
    }
  }
}