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js DNA动态序列比对代码

　　本文标签：DNA,动态序列

<title>动态序列比对</title> 
<script> 
function pairaln(seq1, seq2){ 
// scoring scheme

var MATCH = 1; // +1 for letters that match 
var MISMATCH = -1; // -1 for letters that mismatch 
var GAP = -1; // -1 for any gap 
// initialization

var score=[[]]; 
var pointer=[[]]; 
score[0][0] = 0; 
pointer[0][0] = 0; 
var l1=seq1.length 
var l2=seq2.length

for(var j = 1; j <= l1; j++) {

score[0][j] = GAP * j; 
pointer[0][j] = 2; 
} 
for (var i = 1; i <= l2; i++) {

score[i]=[]; 
pointer[i]=[]; 
score[i][0] = GAP * i; 
pointer[i][0] = 3; 
} 
// fill

for(var i = 1; i <= l2; i++) { 
var letter2 = seq2.charAt(i-1);

for(var j = 1; j <= l1; j++) {

var diagonal_score, left_score, up_score; 
// calculate match score

var letter1 = seq1.charAt(j-1);

if (letter1 == letter2) {

diagonal_score = score[i-1][j-1] + MATCH; 
}

else { 
diagonal_score = score[i-1][j-1] + MISMATCH; 
} 
// calculate gap scores

up_score = score[i-1][j] + GAP; 
left_score = score[i][j-1] + GAP; 
// choose best score

if (diagonal_score >= up_score) {

if (diagonal_score >= left_score) {

score[i][j] = diagonal_score; 
pointer[i][j] = 1; 
}

else { 
score[i][j] = left_score; 
pointer[i][j] = 2; 
}

} else {

if (up_score >= left_score) {

score[i][j] = up_score; 
pointer[i][j] = 3; 
}

else { 
score[i][j] = left_score; 
pointer[i][j] = 2; 
} 
} 
} 
} 
// trace-back

var align1 = []; 
var align2 = []; 
// start at last cell of matrix 
var j = l1; 
var i = l2; 
while (1) {

if(pointer[i][j] == 0)break // ends at first cell of matrix 
if (pointer[i][j] == 1) {

align1[align1.length] = seq1.charAt(j-1); 
align2[align2.length] = seq2.charAt(i-1); 
i--; 
j--; 
}

if (pointer[i][j] == 2) {

align1[align1.length] = seq1.charAt(j-1); 
align2[align2.length] = "-"; 
j--; 
}

if (pointer[i][j] == 3) {

align1[align1.length] = "-"; 
align2[align2.length] = seq2.charAt(i-1); 
i--; 
} 
} 
align1 = align1.reverse(); 
align2 = align2.reverse(); 
return "序列：<p>"+seq1+"<br>"+seq2+"<p>比对结果：<table><tr><td>"+align1.join("</td><td>")+"</td></tr><tr><td>"+align2.join("</td><td>")+"</tr></table>" 
} 
document.write(pairaln(CTGGGCTGACTGA, GACTAGCTAGACTGA)) 
</script>

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