BioJava:CookBook:Distribution:RandomSeqs

From BioJava

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.

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();
    }
  }
}