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JavaScript code to demonstrate an object-oriented approach. The code translates DNA sequence into amino acids and deals with IUPAC-specified base ambiguities.
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‎TranslateDna.js‎

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/*
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JavaScript object that translates a DNA input sequence into a protein sequence.
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It uses the "Combination Constructor/Prototype Pattern" as described in the book "Professional JavaScript For Web Developers"
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by Nicholas Zakas.
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The code is described in link "http://www.javascript-spreadsheet-programming.com/2012/12/object-oriented-javascript-example.html".
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The scientific background is given in "http://www.javascript-spreadsheet-programming.com/2012/11/using-github-for-javascript-and-vba.html"
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USE:
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Useful if you wish to translate a DNA sequence that contains IUPAC ambiguity codes.
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To use (Executed by Node.js): Append the three code lines below to the code file and execute from the command line with:
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node TranslateDna.js
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var seq = 'CCTKAGATCACTCTTTGGCAACGACCCCTCGTCACAATAAAGATAGGGGGGCAACTAAAGGAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAATTTGCCAGGAAGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGATCAGATACTCATAGAAATCTGTGGACATAAAGCTATAGGTACAGTATTAATAGGACCTACACCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGCTTGGTTGCACTTTAAATTTT';
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var trans = new TranslateDna(seq);
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console.log(trans.getAminoAcids());
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Passes JSLint without error when using the default settings.
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*/
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// Constructor function sets instance variables.
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function TranslateDna(dnaSeq) {
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'use strict';
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this.dnaSeq = dnaSeq.toUpperCase();
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this.UNKNOWN = 'X';
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this.translateTable = {'GCT': 'A', 'GCC': 'A', 'GCA': 'A', 'GCG': 'A', 'CGT': 'R', 'CGC': 'R', 'CGA': 'R', 'CGG': 'R', 'AGA': 'R', 'AGG': 'R', 'AAT': 'N', 'AAC': 'N', 'GAT': 'D', 'GAC': 'D', 'TGT': 'C', 'TGC': 'C', 'CAA': 'Q', 'CAG': 'Q', 'GAA': 'E', 'GAG': 'E', 'GGT': 'G', 'GGC': 'G', 'GGA': 'G', 'GGG': 'G', 'CAT': 'H', 'CAC': 'H', 'ATT': 'I', 'ATC': 'I', 'ATA': 'I', 'TTA': 'L', 'TTG': 'L', 'CTT': 'L', 'CTC': 'L', 'CTA': 'L', 'CTG': 'L', 'AAA': 'K', 'AAG': 'K', 'ATG': 'M', 'TTT': 'F', 'TTC': 'F', 'CCT': 'P', 'CCC': 'P', 'CCA': 'P', 'CCG': 'P', 'TCT': 'S', 'TCC': 'S', 'TCA': 'S', 'TCG': 'S', 'AGT': 'S', 'AGC': 'S', 'ACT': 'T', 'ACC': 'T', 'ACA': 'T', 'ACG': 'T', 'TGG': 'W', 'TAT': 'Y', 'TAC': 'Y', 'GTT': 'V', 'GTC': 'V', 'GTA': 'V', 'GTG': 'V', 'TAG': '*', 'TGA': '*', 'TAA': '*'};
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this.iupacAmbiCodes = {'A': ['A'], 'C': ['C'], 'G': ['G'], 'T': ['T'], 'U': ['U'], 'M': ['A', 'C'], 'R': ['A', 'G'], 'W': ['A', 'T'], 'S': ['C', 'G'], 'Y': ['C', 'T'], 'K': ['G', 'T'], 'V': ['A', 'C', 'G'], 'H': ['A', 'C', 'T'], 'D': ['A', 'G', 'T'], 'B': ['C', 'G', 'T'], 'X': ['G', 'A', 'T', 'C'], 'N': ['G', 'A', 'T', 'C']};
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}
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TranslateDna.prototype = {
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constructor: TranslateDna,
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// Perform lookup to return an amino acid for a given nucleotide triplet.
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getAminoAcid: function (codon) {
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'use strict';
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return this.translateTable[codon];
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},
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// Longest and most complex method. Used to disambiguate mixed triplets.
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getCodonsFromAmbiguous: function (ambiguousCodon) {
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'use strict';
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var codons = [],
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first = this.iupacAmbiCodes[ambiguousCodon.charAt(0)],
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lenFirst = first.length,
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second = this.iupacAmbiCodes[ambiguousCodon.charAt(1)],
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lenSecond = second.length,
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third = this.iupacAmbiCodes[ambiguousCodon.charAt(2)],
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lenThird = third.length,
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nuc1,
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nuc2,
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nuc3,
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codon,
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i,
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j,
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k;
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for (i = 0; i < lenFirst; i += 1) {
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nuc1 = first[i];
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for (j = 0; j < lenSecond; j += 1) {
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nuc2 = second[j];
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for (k = 0; k < lenThird; k += 1) {
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nuc3 = third[k];
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codon = nuc1 + nuc2 + nuc3;
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codons.push(codon);
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}
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}
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}
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return codons;
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},
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// Break the instance DNA sequence string into triplets (codons). Assumes the DNA is in-frame.
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splitSequenceIntoTriplets: function () {
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'use strict';
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var i = 0,
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seqLen = this.dnaSeq.length,
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triplets = [],
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triplet;
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for (i = 0; i < seqLen; i += 3) {
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triplet = this.dnaSeq.slice(i, 3 + i);
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triplets.push(triplet);
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}
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this.triplets = triplets;
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},
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//Return an array of triplets, if the instance is set, return it, else generate the triplets array and return it.
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getTriplets: function () {
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'use strict';
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if (!this.triplets) {
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this.splitSequenceIntoTriplets();
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}
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return this.triplets;
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},
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getAminoAcids: function () {
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'use strict';
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var triplets = this.getTriplets(),
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tripletCount = triplets.length,
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aminoAcids = [],
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aminoAcid,
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mixedTriplets = [],
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mixedAminoAcids = [],
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i,
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j;
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for (i = 0; i < tripletCount; i += 1) {
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//Match only triplets composed of the four standard DNA nucleotide bases.
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if (triplets[i].match(/[ACGT]{3}/)) {
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aminoAcid = this.translateTable[triplets[i]];
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aminoAcids.push(aminoAcid);
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} else {
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//Allowable characters in input (four standard nucleotides A,C,G,T and all recognized IUPAC mixture codes).
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if (triplets[i].match(/[ACGTUMRWSYKVHDBXN]{3}/)) {
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mixedTriplets = this.getCodonsFromAmbiguous(triplets[i]);
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for (j = 0; j < mixedTriplets.length; j += 1) {
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aminoAcid = this.translateTable[mixedTriplets[j]];
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if (mixedAminoAcids.indexOf(aminoAcid) === -1) {
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mixedAminoAcids.push(aminoAcid);
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}
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}
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aminoAcids.push(mixedAminoAcids);
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} else {
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aminoAcids.push(this.UNKNOWN);
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}
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}
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}
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return aminoAcids;
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}
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};

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