BioJava:Cookbook:Sequence:Reverse

From BioJava

How do I Reverse Complement a Sequence or SymbolList?

To reverse complement a DNA SymbolList or Sequence simply use the DNATools.reverseComplement(SymbolList sl) method. An equivalent method is found in RNATools for performing the same operation on RNA based Sequences and SymbolLists.

import org.biojava.bio.symbol.*;
import org.biojava.bio.seq.*;
 
public class ReverseComplement {
  public static void main(String[] args) {
 
    try {
      //make a DNA SymbolList
      SymbolList symL = DNATools.createDNA("atgcacgggaactaa");
 
      //reverse complement it
      symL = DNATools.reverseComplement(symL);
 
      //prove that it worked
      System.out.println(symL.seqString());
    }
    catch (IllegalSymbolException ex) {
      //this will happen if you try and make the DNA  seq using non IUB symbols
      ex.printStackTrace();
    }catch (IllegalAlphabetException ex) {
      //this will happen if you try and reverse complement a non DNA (RNA) sequence using DNATools (RNATools)
      ex.printStackTrace();
    }
  }
}