nw

Documentation

Overview

Needleman-Wunsch sequence alignment package

Index

• Variables
• type Aligner
  • func (self *Aligner) Align(reference, query *seq.Seq) (aln seq.Alignment, err error)

Examples

• Aligner.Align

Variables

var LookUpN, LookUpR, LookUpP util.CTL

Default character table lookups.

Types

type Aligner

type Aligner struct {
	Matrix  [][]int
	GapChar byte
	LookUp  util.CTL
}

Needleman-Wunsch aligner type. Matrix is a square scoring matrix with the last column and last row specifying gap penalties. GapChar is the character used to fill gaps. LookUp is used to translate sequance values into positions in the scoring matrix. Currently gap opening is not considered.

func (*Aligner) Align

func (self *Aligner) Align(reference, query *seq.Seq) (aln seq.Alignment, err error)

Method to align two sequences using the Smith-Waterman algorithm. Returns an alignment or an error if the scoring matrix is not square.

Example

nwsa := &seq.Seq{Seq: []byte("AGACTAGTTA")}
nwsb := &seq.Seq{Seq: []byte("GACAGACG")}

//  	 A	 C	 G	 T	 -
// A	10	-3	-1	-4	-5
// C	-3	 9	-5	 0	-5
// G	-1	-5	 7	-3	-5
// T	-4	 0	-3	 8	-5
// -	-5	-5	-5	-5	 0
nwm := [][]int{
	{10, -3, -1, -4, -5},
	{-3, 9, -5, 0, -5},
	{-1, -5, 7, -3, -5},
	{-4, 0, -3, 8, -5},
	{-4, -4, -4, -4, 0},
}

needle := &Aligner{Matrix: nwm, LookUp: LookUpN, GapChar: '-'}
if nwa, err := needle.Align(nwsa, nwsb); err == nil {
	fmt.Printf("%s\n%s\n", nwa[0].Seq, nwa[1].Seq)
}

Output:
AGACTAGTTA
-GAC-AGACG