index.html

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

// Variable statement
var Match = +2;
var Mismatch = -1;
var gap = -2;

var s0 = 'CCUGCAACUUAGGCAGG';

s0 = complement(s0);

var s1 = 'AAGCCAAGCCAAGCCAAGCCGGACGUUGAAUCCGUCCCCCCCAA';
    
var AlignmentA = "";
var AlignmentM = "";
var AlignmentB = "";

var e = '&emsp;';

var m = [];
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]=[];

    for(var j=0; j<=n_1; j++) {

        m[i][j]=0;

        if (i==1 && j>1) {m[i][j]=m[i][j-1]+gap;}
        if (j==1 && i>1) {m[i][j]=m[i-1][j]+gap;}

        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];
    
    A = m[i-1][j-1] + f(Ai, Bj);
    B = m[i-1][j] + gap;
    C = m[i][j-1] + gap;

    if(i>=2 && j>=2 && m[i][j]==A) {

        AlignmentA = Ai + AlignmentA;
        AlignmentB = Bj + AlignmentB;
        
        if(Ai==Bj){
            AlignmentM = '|' + AlignmentM;
        } else {
            AlignmentM = e + AlignmentM;
        }
        
        i = i - 1;
        j = j - 1;

    } else {
        
        if(i>=2 && m[i][j]==B) {
            AlignmentA = Ai + AlignmentA;
            AlignmentB = '-' + AlignmentB;
            AlignmentM = e + AlignmentM;
            i = i - 1;

        } else {
            AlignmentA = '-' + AlignmentA;
            AlignmentB = Bj + AlignmentB;
            AlignmentM = e + AlignmentM;
            j = j - 1;
        }
    }
    
    var r1 = i-1;
    var r2 = j-1;

    if(m[i][j]<=0){break;}
}

// LAYOUT
var tM='';
var tS='';

// Check the end
AlignmentA = AlignmentA + s0.substr(x-1, n_0 - x);
AlignmentB = AlignmentB + s1.substr(y-1, n_1 - y);

// Check the beginning
AlignmentA = s0.substr(0, r1) + AlignmentA;
AlignmentB = s1.substr(0, r2) + AlignmentB;

if(r1>r2){
    var v = r1 - r2;
    
    for(var u=1; u<=v; u++) {tS = tS + e;}
    for(var u=1; u<=v+r2; u++) {tM = tM + e;}
    
    AlignmentB = tS + AlignmentB;
    AlignmentM = tM + AlignmentM;
} else {
    var v = r2 - r1;
    
    for(var u=1; u<=v; u++) {tS = tS + e;}
    for(var u=1; u<=v+r1; u++) {tM = tM + e;}
    
    AlignmentA = tS + AlignmentA;
    AlignmentM = tM + AlignmentM;
}

// Print the alignment
document.write(complement(AlignmentA) + '<br>');
document.write(AlignmentM + '<br>');
document.write(AlignmentB + '<br>');

// Matching function
function f(a1, a2) {
    if(a1 === a2){return Match;} else {return Mismatch;}
}

// Make complementarity
function complement(c) {

    c = c.replace(/C/g,'1');
    c = c.replace(/G/g,'2');
    c = c.replace(/A/g,'3');
    c = c.replace(/U/g,'4');

    c = c.replace(/1/g,'G');
    c = c.replace(/2/g,'C');
    c = c.replace(/3/g,'U');
    c = c.replace(/4/g,'A');

    return c;
}

</script>