jaligner.SmithWatermanGotoh Class Reference

Static Public Member Functions
static Alignment	align (Sequence s1, Sequence s2, Matrix matrix, float o, float e)

Detailed Description

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.nosp@m.@use.nosp@m.rs.sf.nosp@m..net)

Member Function Documentation

static Alignment jaligner.SmithWatermanGotoh.align ( Sequence  s1, Sequence  s2, Matrix  matrix, float  o, float  e  )

static

Logger 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

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The documentation for this class was generated from the following file:

• java/jaligner/SmithWatermanGotoh.java