How can I generate a random Sequence from a Distribution?

BioJava Distribution objects have a method for sampling Symbols. By successively sampling enough Symbols you can build up a random sequence. Because this is a common task a static method is provided in DistributionTools called generateSequence().

The following program generates a random Sequence using a uniform Distribution over the DNA Alphabet. The emitted sequence will differ each time although its composition should be close to 25% of each residue. Non uniform distributions can be used to generate biased sequences.

```java import org.biojava.bio.dist.*; import org.biojava.bio.seq.*; import org.biojava.bio.seq.io.*; import java.io.*;

public class RandomSequence {

 public static void main(String[] args) {

   //make a uniform distribution over the DNA Alphabet
   Distribution dist = new UniformDistribution(DNATools.getDNA());

   //generate a 700bp random sequence
   Sequence seq = DistributionTools.generateSequence("random seq", dist, 700);

   try {
     //print it to STDOUT
     SeqIOTools.writeFasta(System.out, seq);
   }
   catch (IOException ex) {
     //io error
     ex.printStackTrace();
   }
 }

} ```