JavaScript DNA动态序列比对代码

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引入JS
- 3.0.0 2.2.0 2.1.4 2.1.3 2.1.2 2.1.1 2.1.0 2.0.3 2.0.2 2.0.1 2.0.0 1.12.0 1.11.3 1.11.2 1.11.1 1.11.0 1.10.2 1.10.1 1.10.0 1.9.1 1.9.0 1.8.3 1.8.2 1.8.1 1.8.0 1.7.2 1.7.1 1.7 1.6.4 1.6.2 1.6.1 1.4.4 1.4.3 1.4.2 1.4.1 1.4.0
- 1.7.3 1.7.2 1.7.1.0 1.7.0.0
- 2.0.0-beta.0 2.0.0-alpha.55 1.5.0-rc.0 1.4.8 1.4.0 1.3.20 1.2.29 1.1.5 1.0.8
- 1.8.3 1.7.0 1.6.0 1.5.2 1.4.4 1.3.3 1.2.4 1.1.7
- 1.10.4 1.9.7 1.8.10 1.7.8 1.6.3 1.5.4 1.4.6 1.3.3
- core1.6.0 core-compat1.6.0 core1.5.2 core-compat1.5.2 core-full-compat-yc1.4.5 core-full-compat1.4.5 core-full-nocompat-yc1.4.5 core-full-nocompat1.4.5
- 1.4.2 1.4.1 1.4.0 1.3.0 1.2.0 1.1.0
- 3.7.3 3.7.2 3.7.1 3.7.0 3.7 3.6.2 3.6.1 3.6

引入框架
- 1.4.5 1.4.4 1.4.3 1.4.2 1.4.1 1.4.0 1.3.2
- 1.11.4 1.11.3 1.11.2 1.11.1 1.11.0 1.10.4 1.10.3 1.10.2
- 3.3.6 3.3.5 3.3.0 3.2.0 2.3.2

汉王

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<title>动态序列比对</title>
<script>
function pairaln(seq1, seq2){
	var MATCH    =  1; // +1 for letters that match
	var MISMATCH = -1; // -1 for letters that mismatch
	var GAP      = -1; // -1 for any gap
	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;
	}
	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;
        		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;
        		}

up_score   = score[i-1][j] + GAP;
        		left_score = score[i][j-1] + GAP;
        		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;
            			}
        		}
    		}
	}
	var align1 = [];
	var align2 = [];
	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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JS代码

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名称

JavaScript DNA动态序列比对代码

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描述

JavaScript动态序列比对代码，随便写着玩的，在网上见到用VC、VB写的比较多，这个算法以前在高中课本上见到过，我只是用Js写一下试试，或许还不是太准确。