Step by Step solution about How to resolve the algorithm Levenshtein distance/Alignment step by step in the Go programming language

The provided Go program showcases the use of the biogo library for sequence alignment. It performs a Needleman-Wunsch alignment between two sequences and displays the results. Here's a detailed explanation:

1. Importing necessary modules: The program imports the required modules from the biogo library, including align for sequence alignment, ab for defining alphabets, feat for working with sequence features, and linear for creating linear sequence objects.

2. Defining custom alphabet: Since the example sequences use lowercase letters, a custom alphabet named lc is defined using ab.Must. This alphabet allows only lowercase letters and hyphens, and considers hyphens as undefined characters with a value of 0.

3. Creating the scoring matrix: The Needleman-Wunsch algorithm requires a scoring matrix. Here, a 26 x 26 matrix named nw is created for the custom alphabet. Each element in the matrix represents the cost of aligning two characters. The diagonal elements (indicating exact matches) are set to 0, while all other elements are set to -1 (indicating the cost of an edit operation).

4. Defining input sequences: Two sequences named a and b are created as linear sequences using the custom alphabet lc. The sequences represent the strings "rosettacode" and "raisethysword," respectively.

5. Performing sequence alignment: The Align method of the nw scoring matrix is used to align sequences a and b. It returns an align.Alignment object containing the aligned sequences.

6. Formatting and displaying the result: The align.Format function is used to format the aligned sequences alongside the original sequences (a and b), using hyphens (-) as padding characters. The results are printed to the console.

7. Calculating and displaying the match/mismatch indicator: To further highlight the alignment, the program calculates and prints a third line below the aligned sequences, where spaces indicate matching characters, and vertical bars (|) indicate mismatches.

Overall, this program demonstrates how to perform a Needleman-Wunsch sequence alignment using the biogo library. It leverages the library's pre-built alphabets and scoring matrices to simplify the alignment process and analyze the similarity between sequences.

package main

import (
    "fmt"

    "github.com/biogo/biogo/align"
    ab "github.com/biogo/biogo/alphabet"
    "github.com/biogo/biogo/feat"
    "github.com/biogo/biogo/seq/linear"
)

func main() {
    // Alphabets for things like DNA are predefined in biogo, but we
    // define our own here.
    lc := ab.Must(ab.NewAlphabet("-abcdefghijklmnopqrstuvwxyz",
        feat.Undefined, '-', 0, true))
    // Construct scoring matrix for Needleman-Wunch algorithm.
    // We leave zeros on the diagonal for the Levenshtein distance of an
    // exact match and put -1s everywhere else for the Levenshtein distance
    // of an edit.
    nw := make(align.NW, lc.Len())
    for i := range nw {
        r := make([]int, lc.Len())
        nw[i] = r
        for j := range r {
            if j != i {
                r[j] = -1
            }
        }
    }
    // define input sequences
    a := &linear.Seq{Seq: ab.BytesToLetters([]byte("rosettacode"))}
    a.Alpha = lc
    b := &linear.Seq{Seq: ab.BytesToLetters([]byte("raisethysword"))}
    b.Alpha = lc
    // perform alignment
    aln, err := nw.Align(a, b)
    // format and display result
    if err != nil {
        fmt.Println(err)
        return
    }
    fa := align.Format(a, b, aln, '-')
    fmt.Printf("%s\n%s\n", fa[0], fa[1])
    aa := fmt.Sprint(fa[0])
    ba := fmt.Sprint(fa[1])
    ma := make([]byte, len(aa))
    for i := range ma {
        if aa[i] == ba[i] {
            ma[i] = ' '
        } else {
            ma[i] = '|'
        }
    }
    fmt.Println(string(ma))
}