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<!-- # John Wiley & Sons, Inc. # -->

<!-- # # -->

<!-- # Book: Algorithms in Bioinformatics: Theory and Implementation # -->

<!-- # Author: Dr. Paul A. Gagniuc # -->

<!-- # # -->

<!-- # Institution: # -->

<!-- # University Politehnica of Bucharest # -->

<!-- # Faculty of Engineering in Foreign Languages # -->

<!-- # Department of Engineering in Foreign Languages # -->

<!-- # # -->

<!-- # Area: European Union # -->

<!-- # Date: 04/01/2021 # -->

<!-- # # -->

<!-- # Cite this work as: # -->

<!-- # Paul A. Gagniuc. Algorithms in Bioinformatics: Theory and Implementation. John Wiley & Sons, 2021, ISBN: 9781119697961. # -->

<!-- # # -->

<!-- ############################################################################################################################## -->

<script>

// AN IMPLEMENTATION BASED ON ZERO VALUES

var c = "GAAGTGAGT,TTCGTAAGT,AAGGTACTT,CTGGTGAGC,AGAGTGAGT," +

"CAGGTAGAG,ACTGTACGT,CTGGTGAGT,TATGTAAGT,CGGGTGAGC";

var s = [];

var m = [];

m = c.split(',');

var n = m.length;

//THE ALIGNMENT MATRIX

for(var i=0; i<n; i++){

s[i] = [];

s[i]=m[i].split('');

}

//ALPHABET DETECTION

var a = [];

var t = c.replace(/,/g, '').split('');

var k = t.length;

for(var i=0; i<=k; i++){

var q = 1;

for(var j=0; j<=a.length; j++){

if (t[i] === a[j]) {q = 0;}

}

if (q === 1) {a.push(t[i]);}

}

// PROFILE MATRIX INITIALIZATION

var p = [];

for(var h=0; h<a.length; h++){

p[h]=[];

for(var i=0; i<=s[0].length; i++) {

p[h][i]=0;

p[h][0]=a[h];

}

}

// THE POSITION FREQUENCY MATRIX

for(var i=0; i<s.length; i++) {

for(var j=0; j<s[i].length; j++){

for(var h=0; h<a.length; h++){

if (s[i][j] === a[h]) {p[h][j+1]++;}

}

}

}

// POSITION PROBABILITY MATRIX & POSITION WEIGHT MATRIX

for(var i=0; i<p.length; i++) {

for(var j=0; j<p[i].length-1; j++){

if(p[i][j+1]==0){

p[i][j+1]=0;

} else {

var g = p[i][j+1]/s.length;

p[i][j+1]=Math.log(g/0.25).toFixed(2);

}

}

}

// SEARCH MOTIF IN Z

var z = "AAAAAACAGGTGAGTAAAAAAAA";

var r = '';

var w = '';

var u = z.length - s.length + 2;

for(var l=0; l<u; l++) {

w = z.substr(l, s.length-1);

var d = w.split('');

var score = 0;

for(var f=0; f<d.length; f++){

for(var h=0; h<a.length; h++){

if(d[f]==p[h][0])

{

score += Number(p[h][f+1]);

}

}

}

if(score<0){score=0;}

r += score.toFixed(0) + ',';

}

document.write(r);

</script>