jaligner.NeedlemanWunsch Class Reference

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

Detailed Description

An implementation of the Needleman-Wunsch algorithm for biological global pairwise sequence alignment.

Reference: Advanced Dynamic Programming Tutorial.

Author

Ahmed Moustafa

Member Function Documentation

static Alignment jaligner.NeedlemanWunsch.align ( Sequence  s1, Sequence  s2, Matrix  matrix, float  gap  )

static

Aligns two sequences by Needleman-Wunsch (global)

Parameters

s1	sequene #1 (Sequence)
s2	sequene #2 (Sequence)
matrix	scoring matrix (Matrix)
gap	open 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/NeedlemanWunsch.java