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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>

// MAIN SEQUENCE

var z = 'ATCGATTCGATATCAT';

// ORDER

var h = 'ACGT';

// TRAINING MODELS

var s0 = h+'ATCGATTCGATATCATACACGTAT';

var s1 = h+'AATCCTATCTTACTATTCTACTCAGTCCC';

var q;

// get the two transition matrices

var p = [] = DPD(s0, '(+)');

var b = [] = DPD(s1, '(-)');

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

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

if (i>0 && j>0) {

if(p[i][j]==0){p[i][j]=0.000000000000000001;}

if(b[i][j]==0){b[i][j]=0.000000000000000001;}

q = p[i][j]/b[i][j];

p[i][j] = Log(2,q).toFixed(2);

}

}

}

document.write('log likelihood:<br>'+SMC(p)+'<hr>');

var l = [];

var f='';

var t=0;

l[0]="";

l[1]="";

for(var u=0; u<z.length; u++){

l[0] = z.substr(u, 1);

l[1] = z.substr(u + 1, 1);

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

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

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

f+='(' + Number(p[i][j]) + ')+';

t+=Number(p[i][j]);

}

}

}

}

document.write(z+'<br>');

document.write(f+' = '+t);

</script>