align

Documentation

Index

• func NeedlemanWunsch(stringA string, stringB string, scoring Scoring) (int, string, string)
• type Scoring
  • func NewScoring() Scoring

Examples

• NeedlemanWunsch

Functions

func NeedlemanWunsch

func NeedlemanWunsch(stringA string, stringB string, scoring Scoring) (int, string, string)

NeedlemanWunsch performs global alignment between two strings using the Needleman-Wunsch algorithm. It returns the final score and the optimal alignments of the two strings in O(nm) time and O(nm) space. https://en.wikipedia.org/wiki/Needleman-Wunsch_algorithm

Example

package main

import (
	"fmt"

	"github.com/TimothyStiles/poly/align"
)

func main() {
	a := "GATTACA"
	b := "GCATGCU"
	scoring := align.NewScoring()
	score, alignA, alignB := align.NeedlemanWunsch(a, b, scoring)
	fmt.Printf("score: %d, A: %s, B: %s", score, alignA, alignB)
}

Types

type Scoring

type Scoring struct {
	Match      int
	Mismatch   int
	GapPenalty int
}

Scoring is a struct that holds the scoring matrix for match, mismatch, and gap penalties.

func NewScoring

func NewScoring() Scoring

NewScoring returns a new Scoring struct with default values.