RecursiveSeqAlign.js

//The two sequences to compare
var sequence1 = "ATGCGAATCGC"
var sequence2 = "ATCCTACCG"

//Creates multi-dimensional array dependent on sequence lengths
var arr = new Array(sequence2.length + 1)
for (i = 0; i < sequence2.length + 1; i++) {
    arr[i] = new Array(sequence1.length + 1);
}

//Fills array with 0s
for (i = 0; i < arr.length; i++) {
    var col = i;
    for (j = 0; j < arr[col].length; j++) {
        arr[col][j] = 0;
    }
}

//Matrix Fill
for (i = 1; i < arr.length; i++) {
    var col = i;
    for (j = 1; j < sequence1.length + 1; j++) {
        arr[col][j] = -10000
        if (arr[col][j - 1] - 2 > arr[col][j]) {
            arr[col][j] = arr[col][j - 1] - 2;
        }
        if (arr[col - 1][j] - 2 > arr[col][j]) {
            arr[col][j] = arr[col - 1][j] - 2;
        }
        var match = 0;
        if (sequence2[col - 1] == sequence1[j - 1]) {
            match = 2;
        } else {
            match = -1;
        }
        if ((arr[col - 1][j - 1] + match) > arr[col][j]) {
            arr[col][j] = (arr[col - 1][j - 1]) + match;
        }
    }
}

console.table(arr);

//Declares traceback array and pushObject function
var traceback = [];
var pushObj = function(value, direction, seq2, seq1, div) {
    traceback.push({
        pos: value,
        dir: direction,
        seq2: seq2,
        seq1: seq1
    })
}

//Traceback
Col = arr.length - 1;
Row = sequence1.length;

function tracefunc(traceCol, traceRow) {
    if (traceCol > 0 && traceRow > 0) {
        if (sequence2[traceCol - 1] == sequence1[traceRow - 1]) {
            pushObj(arr[traceCol][traceRow], "diag", sequence2[traceCol - 1], sequence1[traceRow - 1]);
            tracefunc(traceCol - 1, traceRow - 1);

        } else if (arr[traceCol][traceRow] == ((arr[traceCol - 1][traceRow]) - 2)) {
            pushObj(arr[traceCol][traceRow], "up", sequence2[traceCol - 1], "_");
            tracefunc(traceCol - 1, traceRow);
        } else if (arr[traceCol][traceRow] == ((arr[traceCol][traceRow - 1]) - 2)) {
            pushObj(arr[traceCol][traceRow], "left", "_", sequence1[traceRow - 1]);
            tracefunc(traceCol, traceRow - 1);
        } else {
            pushObj(arr[traceCol][traceRow], "diag", "m", "m")
            tracefunc(traceCol - 1, traceRow - 1);
        }

    } else if (traceCol > 0) {
        pushObj(arr[traceCol][traceRow], "up", sequence2[traceCol - 1], "_")
        tracefunc(traceCol - 1, traceRow);
    } else if (traceRow > 0) {
        pushObj(arr[traceCol][traceRow], "left", "_", sequence1[traceRow - 1]);
        tracefunc(traceCol, traceRow - 1);
    }
}
tracefunc(Col, Row);

//Console.log results
var align1 = "";
var align2 = "";
for (i = 0; i < traceback.length; i++) {
    align1 = traceback[i].seq1 + align1;
    align2 = traceback[i].seq2 + align2;
}
console.log(align1)
console.log(align2)