Class SuffixTree

java.lang.Object
org.biojava.bio.symbol.SuffixTree
All Implemented Interfaces:
Serializable

public class SuffixTree extends Object implements Serializable
Suffix tree implementation. The interface is a bit strange, as it needed to be as space-efficient as possible. More work could be done on the space issue.

A suffix tree is an efficient method for encoding the frequencies of motifs in a sequence. They are sometimes used to quickly screen for similar sequences. For instance, all motifs of length up to 2 in the sequence AAGT could be encoded as:

 root(4)
 |
 A(2)--------G(1)-----T(1)
 |           |
 A(1)--G(1)  T(1)
 

A possible method of comparing SuffixTrees is provided as a kernel function as org.biojava.stats.svm.tools.SuffixTreeKernel.

Author:
Matthew Pocock, Thomas Down (documentation and other updates)
See Also: