BioJava:CookBook:DP:WeightMatrix

From BioJava

How do I use a WeightMatrix to find a motif?

A Weight Matrix is a useful way of representing an alignment or a motif. It can also be used as a scoring matrix to detect a similar motif in a sequence. BioJava contains a class call WeightMatrix in the org.biojava.bio.dp package. There is also a WeightMatrixAnnotator which uses the WeightMatrix to add Features to any portion of the sequence being searched which exceed the scoring threshold.

The following program generates a WeightMatrix from an aligment and uses that matrix to annotate a Sequence with a threshold of 0.1

import java.util.*;
 
import org.biojava.bio.dist.*;
import org.biojava.bio.dp.*;
import org.biojava.bio.seq.*;
import org.biojava.bio.symbol.*;
 
public class WeightMatrixDemo {
  public static void main(String[] args) throws Exception{
    //make an Alignment of a motif.
    Map map = new HashMap();
    map.put("seq0", DNATools.createDNA("aggag"));
    map.put("seq1", DNATools.createDNA("aggaa"));
    map.put("seq2", DNATools.createDNA("aggag"));
    map.put("seq3", DNATools.createDNA("aagag"));
    Alignment align = new SimpleAlignment(map);
 
    //make a Distribution[] of the motif
    Distribution[] dists =
        DistributionTools.distOverAlignment(align, false, 0.01);
 
    //make a Weight Matrix
    WeightMatrix matrix = new SimpleWeightMatrix(dists);
 
    //the sequence to score against
    Sequence seq = DNATools.createDNASequence("aaagcctaggaagaggagctgat","seq");
 
    //annotate the sequence with the weight matrix using a low threshold (0.1)
    WeightMatrixAnnotator wma = new WeightMatrixAnnotator(matrix, 0.1);
    seq = wma.annotate(seq);
 
    //output match information
    for (Iterator it = seq.features(); it.hasNext(); ) {
      Feature f = (Feature)it.next();
      Location loc = f.getLocation();
      System.out.println("Match at " + loc.getMin()+"-"+loc.getMax());
      System.out.println("\tscore : "+f.getAnnotation().getProperty("score"));
    }
  }
}