jaligner
Class NeedlemanWunschGotoh

java.lang.Object
  jaligner.NeedlemanWunschGotoh

public final class NeedlemanWunschGotoh

extends java.lang.Object

An implementation of the Needleman-Wunsch algorithm with Gotoh's improvement for biological global pairwise sequence alignment.

Author:

Bram Minnaert, Ahmed Moustafa

Method Summary

static Alignment

align(Sequence s1, Sequence s2, Matrix matrix, float o, float e) Aligns two sequences by Needleman-Wunsch (global)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Method Detail

align

public static Alignment align(Sequence s1,
                              Sequence s2,
                              Matrix matrix,
                              float o,
                              float e)

Aligns two sequences by Needleman-Wunsch (global)

Parameters:

s1 - sequene #1 (Sequence)

s2 - sequene #2 (Sequence)

matrix - scoring matrix (Matrix)

o - open gap penalty

e - extend gap penalty

Returns:

alignment object contains the two aligned sequences, the alignment score and alignment statistics

See Also:

Sequence, Matrix