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Additional algorithm 16.html
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Additional algorithm 16.html
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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. # -->
<!-- # # -->
<!-- ############################################################################################################################## -->
<style>
body {
padding: 1rem;
font-family: monospace;
font-size: 18px;
font-style: normal;
font-variant: normal;
line-height: 20px;
}
</style>
<script>
// declaratie variabile
var s0 = 'TGAATTCAGTTA';
var s1 = 'TGGATCGA';
var Match = +2;
var Mismatch = -1;
var gap = -2;
var AlignmentA = "";
var AlignmentM = "";
var AlignmentB = "";
var m = [];
var t = [];
var s = [];
var MMax = 0;
var MMin = 0;
var x = 0;
var y = 0;
// Matrix initialization and completion
s[0] = [] = s0.split('');
s[1] = [] = s1.split('');
var n_0 = s[0].length+1;
var n_1 = s[1].length+1;
for(var i=0; i<=n_0; i++) {
m[i]=[];
t[i]=[];
for(var j=0; j<=n_1; j++) {
m[i][j]=0;
t[i][j]=0;
if (i>1) {m[i][0]=t[i][0]=s[0][i-2];}
if (j>1) {m[0][j]=t[0][j]=s[1][j-2];}
if (i>1) {m[i][0]=s[0][i-2];}
if (j>1) {m[0][j]=s[1][j-2];}
if(i>1 && j>1){
var A = m[i-1][j-1] + f(m[i][0],m[0][j]); //'\
var B = m[i-1][j] + gap; //'-
var C = m[i][j-1] + gap; //'|
var D = 0;
m[i][j] = Math.max(A, B, C, D);
if(m[i][j] > MMax){MMax = m[i][j];x=i;y=j;}
if(m[i][j] < MMin){MMin = m[i][j];}
}
}
}
//Traceback & text alignment
var i = x;
var j = y;
while (i>=2 || j>=2) {
var Ai = m[i][0];
var Bj = m[0][j];
if(i>=2 && j>=2 && m[i][j]==m[i-1][j-1] + f(Ai, Bj)) {
t[i][j] = m[i-1][j-1] + f(Ai, Bj);
AlignmentA = Ai + AlignmentA;
AlignmentB = Bj + AlignmentB;
if(Ai==Bj){
AlignmentM = '|' + AlignmentM;
} else {
AlignmentM = ' ' + AlignmentM;
}
i = i - 1;
j = j - 1;
} else {
if(i>=2 && m[i][j]==m[i-1][j] + gap) {
t[i][j] = m[i-1][j] + gap;
AlignmentA = Ai + AlignmentA;
AlignmentB = '-' + AlignmentB;
AlignmentM = ' ' + AlignmentM;
i = i - 1;
} else {
t[i][j] = m[i][j-1] + gap;
AlignmentA = '-' + AlignmentA;
AlignmentB = Bj + AlignmentB;
AlignmentM = ' ' + AlignmentM;
j = j - 1;
}
}
if(m[i][j]<=0){break;}
}
// Print matrix m
document.write(SMC(m) + '<hr>');
document.write(SMC(t) + '<hr>');
// Print the alignment
document.write(AlignmentA + '<br>');
document.write(AlignmentM + '<br>');
document.write(AlignmentB + '<br>');
// Matching function
function f(a1, a2) {
if(a1 === a2){return Match;} else {return Mismatch;}
}
// 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>