Additional algorithm 47.html

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<!-- #  John Wiley & Sons, Inc.                                                                                                   # -->
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<!-- #  Book:   Algorithms in Bioinformatics: Theory and Implementation                                                           # -->
<!-- #  Author: Dr. Paul A. Gagniuc                                                                                               # -->
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<!-- #  Institution:                                                                                                              # -->
<!-- #    University Politehnica of Bucharest                                                                                     # -->
<!-- #    Faculty of Engineering in Foreign Languages                                                                             # -->
<!-- #    Department of Engineering in Foreign Languages                                                                          # -->
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<!-- #  Area:   European Union                                                                                                    # -->
<!-- #  Date:   04/01/2021                                                                                                        # -->
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<!-- #  Cite this work as:                                                                                                        # -->
<!-- #    Paul A. Gagniuc. Algorithms in Bioinformatics: Theory and Implementation. John Wiley & Sons, 2021, ISBN: 9781119697961. # -->
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<script>

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('');
}

// DETECT ALL SYMBOLS USING ARRAYS
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]=0.00000000000000001;
        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]++;}
        }
    }
}

// THE POSITION PROBABILITY MATRIX
for(var i=0; i<p.length; i++) {
    for(var j=0; j<p[i].length-1; j++){
    
        p[i][j+1]=p[i][j+1]/s.length;
        
    }
}

// THE POSITION WEIGHT MATRIX
for(var i=0; i<p.length; i++) {
    for(var j=0; j<p[i].length-1; j++){

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

document.write(SMC(p));

// SHOW MATRIX CONTENT 
function SMC(m) {
    var r = "<table border=1>";
    for(var i=0; i<m.length; i++) {
        r += "<tr>";
        for(var j=0; j<m[i].length; j++){
            r += "<td>"+m[i][j]+"</td>";
        }
        r += "</tr>";
    }
    r += "</table>";

    return r;
}

</script>