JavaScript DNA動態序列比對代碼

2024-09-05 12:17:56

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JavaScript動態序列比對代碼，隨便寫著玩的，在網上見到用VC、VB寫的比較多，這個算法以前在高中課本上見到過，我只是用Js寫一下試試，或許還不是太準確。

<title>動態序列比對</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>比對結果：<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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