Class GuanUberbacher<S extends Sequence<C>,​C extends Compound>

  • Type Parameters:
    S - each Sequence of the alignment pair is of type S
    C - each element of an AlignedSequence is a Compound of type C
    All Implemented Interfaces:
    Aligner<S,​C>, MatrixAligner<S,​C>, PairwiseSequenceAligner<S,​C>, PairwiseSequenceScorer<S,​C>, Scorer

    public class GuanUberbacher<S extends Sequence<C>,​C extends Compound>
    extends AnchoredPairwiseSequenceAligner<S,​C>
    Guan and Uberbacher defined an algorithm for pairwise global sequence alignments (from the first until the last Compound of each Sequence). This class performs such global sequence comparisons efficiently by dynamic programming with a space requirement reduced from quadratic (a multiple of query sequence length times target sequence length) to only linear (a multiple of query sequence length). The counterpoint to this reduction in space complexity is a modest (a multiple < 2) increase in time.
    Mark Chapman