_javascript technique of JS DNA dynamic sequence ratio code

<title> Dynamic sequence Alignment </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 + +) {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] = Diago Nal_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 the last cell of matrix var j = L1; var i = L2; while (1) {if (pointer[i][j] = = 0) break//ends at in the matrix if (pointer[i][j] = 1) {Align1[align1.lengt h] = 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 "Sequence:<P> "+seq1+" <br> "+seq2+" <p> result:<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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