BioJava:Cookbook:Sequence:Reverse
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.
```java 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();
}
}
} ```