-
-
Notifications
You must be signed in to change notification settings - Fork 3
Expand file tree
/
Copy pathAdditional algorithm 15.html
More file actions
155 lines (120 loc) · 5.25 KB
/
Additional algorithm 15.html
File metadata and controls
155 lines (120 loc) · 5.25 KB
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
<!-- ############################################################################################################################## -->
<!-- # 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 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 = [];
// 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 && 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]=t[i][0]=s[0][i-2];}
if (j>1) {m[0][j]=t[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; //'|
m[i][j] = Math.max(A, B, C);
}
}
}
//Traceback
var i = n_0;
var j = n_1;
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(i<=2 && j<=2) {t[i][j] = 0;}
}
document.write(SMC(m) + '<hr>');
document.write(SMC(t) + '<hr>');
document.write(AlignmentA + '<br>');
document.write(AlignmentM + '<br>');
document.write(AlignmentB + '<br>');
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>