Class SuffixTree

  • All Implemented Interfaces:

    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:

     |           |
     A(1)--G(1)  T(1)

    A possible method of comparing SuffixTrees is provided as a kernel function as

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