jaligner
Class SmithWatermanGotoh

java.lang.Object
  jaligner.SmithWatermanGotoh

public final class SmithWatermanGotoh

extends java.lang.Object

An implementation of the Smith-Waterman algorithm with Gotoh's improvement for biological local pairwise sequence alignment. Recursive definition:

• Base conditions:
  • V(0, 0) = 0
  • V(i, 0) = E(i, 0) = Wg + iWs
  • V(0, j) = F(0, j) = Wg + jWs
• Recurrence relation:
  • V(i, j) = max{E(i, j), F(i, j), G(i, j)}, where:
  • G(i, j) = V(i - 1, j - 1) + similarity(Si, Tj)
  • E(i, j) = max{E(i, j - 1) + Ws, V(i, j - 1) + Wg + Ws}
  • F(i, j) = max{F(i - 1, j) + Ws, V(i - 1, j) + Wg + Ws}

Author:

Ahmed Moustafa (ahmed@users.sf.net)

Method Summary

static Alignment

align(Sequence s1, Sequence s2, Matrix matrix, float o, float e) Aligns two sequences by Smith-Waterman (local)

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 Smith-Waterman (local)

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