jaligner.NeedlemanWunschGotoh 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 Needleman-Wunsch algorithm with Gotoh's improvement for biological global pairwise sequence alignment.

Author

Ahmed Moustafa

Bram Minnaert

Version

Revision

1.12

Member Function Documentation

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

static

Aligns two sequences by Needleman-Wunsch (global)

Parameters

s1	sequene #1 (Read)
s2	sequene #2 (Read)
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

Read

Matrix

Here is the call graph for this function:

---

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

• java/jaligner/NeedlemanWunschGotoh.java