Update: I have finally used the implementation of this algorithm in Swift as the first step to create a very simple iOS app to test how the Needleman−Wunsch algorithm works. More details can be found in this repo.

According to Wikipedia:

The Needleman–Wunsch algorithm is an algorithm used in bioinformatics to align protein or nucleotide sequences. It was one of the first applications of dynamic programming to compare biological sequences. The algorithm was developed by Saul B. Needleman and Christian D. Wunsch and published in 1970. The algorithm essentially divides a large problem (e.g. the full sequence) into a series of smaller problems and uses the solutions to the smaller problems to reconstruct a solution to the larger problem. It is also sometimes referred to as the optimal matching algorithm and the global alignment technique. The Needleman–Wunsch algorithm is still widely used for optimal global alignment, particularly when the quality of the global alignment is of the utmost importance.

I recently studied this algorithm in a Computational Genomics class. To reinforce my understanding of it, I coded it using Swift. So here follows a fairly straightforward implementation of the Needleman–Wunsch algorithm in this language:

``````import Foundation

func needlemanWunsch(input1: String, input2: String, match: Int = 5, substitution: Int = -2, gap: Int = -6)
-> (output1: String, output2: String, score: Int) {

enum Origin { case top, left, diagonal }

let seq1 = Array(input1) // Horizontal, so its length sets number of columns (j)
let seq2 = Array(input2) // Vertical, so its length sets number of rows (i)

var scores: [[Int]] = []
var paths: [[[Origin]]] = []

// Initialize both matrixes with zeros.
for _ in 0...seq2.count {
scores.append(Array(repeatElement(0, count: seq1.count + 1)))
paths.append(Array(repeatElement([], count: seq1.count + 1)))
}

// Initialize first rows and columns.
for j in 1...seq1.count {
scores[j] = scores[j - 1] + gap
paths[j] = [.left]
}
for i in 1...seq2.count {
scores[i] = scores[i - 1] + gap
paths[i] = [.top]
}

// Populate the rest of both matrices.
for i in 1...seq2.count {
for j in 1...seq1.count {
let fromTop = scores[i - 1][j] + gap
let fromLeft = scores[i][j - 1] + gap
let fromDiagonal = scores[i - 1][j - 1] + (seq1[j - 1] == seq2[i - 1] ? match : substitution)
let fromMax = max(fromTop, fromLeft, fromDiagonal)

scores[i][j] = fromMax

if fromDiagonal == fromMax { paths[i][j].append(.diagonal) }
if fromTop == fromMax { paths[i][j].append(.top) }
if fromLeft == fromMax { paths[i][j].append(.left) }
}
}

// Get the alignment representation.
var output1 = ""
var output2 = ""

var i = seq2.count
var j = seq1.count

while !(i == 0 && j == 0) {
switch paths[i][j].first! {
case .diagonal:
output1 = String(seq1[j - 1]) + output1
output2 = String(seq2[i - 1]) + output2
i -= 1
j -= 1
case .top:
output1 = "-" + output1
output2 = String(seq2[i - 1]) + output2
i -= 1
case .left:
output1 = String(seq1[j - 1]) + output1
output2 = "-" + output2
j -= 1
}
}

return (output1, output2, scores[seq2.count][seq1.count])
}
``````

And then we can use the `needlemanWunsch` function like this:

``````let alignment = needlemanWunsch(input1: "GATTACA", input2: "GGTACAA")
print(alignment.output1) // GATTAC-A
print(alignment.output2) // G-GTACAA
print(alignment.score)   // 11
``````