net.maizegenetics.analysis.gbs.neobio

Class CrochemoreLandauZivUkelsonLocalAlignment

java.lang.Object

net.maizegenetics.analysis.gbs.neobio.PairwiseAlignmentAlgorithm

net.maizegenetics.analysis.gbs.neobio.CrochemoreLandauZivUkelson

net.maizegenetics.analysis.gbs.neobio.CrochemoreLandauZivUkelsonLocalAlignment

public class CrochemoreLandauZivUkelsonLocalAlignment
extends CrochemoreLandauZivUkelson

This class implements the local pairwise sequence alignment algorithm (with linear gap penalty function) due to Maxime Crochemore, Gad Landau and Michal Ziv-Ukelson (2002).

This implementation derives from the paper of M.Crochemore, G.Landau and M.Ziv-Ukelson, A Sub-quadratic Sequence Alignment Algorithm for Unrestricted Scoring Matrices (available here as PDF or Postscript).

For a general description of the algorithm, please refer to the specification of the abstract CrochemoreLandauZivUkelson superclass.

This class consist mainly of methods that:

create and compute all information of a block (see createBlock and its variants); compute the output border of a block (see computeOutputBorder; locate the score of a high scoring global alignment in the block table (see locateScore; build an optimal global alignment from the information stored in the block table (see buildOptimalAlignment.

This algorithm works essentially in the same way as the global alignment version. The main differences is that an aptimal path can either be contained entirely in a block (called C-path) or be a block-crossing path. A block-crossing path consists of a (possibly empty) S-path (a path that starts inside a block and ends in its output border), followed by any number of paths that cross a block from its input border to its output border, and ending in an E-path (a path that starts in the input border of a block and ends inside the block).

Therefore, it is necessary to compute extra information to keep track of these possibilities. This is accomplished by using an instance of a LocalAlignmentBlock (which extends the AlignmentBlock class) for every block in the block table.

Author:

Sergio A. de Carvalho Jr.

See Also:

CrochemoreLandauZivUkelson, CrochemoreLandauZivUkelsonLocalAlignment