//Written by Paul Stothard, University of Alberta, Canada function pairwiseAlignCodons (theDocument) { //var MATRIX = "codon"; //var GAP_PENALTY = 2; //var BEGIN_GAP_PENALTY = 0; //var END_GAP_PENALTY = 0; var newCodonsOne = ""; var titleOne = ""; var newCodonsTwo = ""; var titleTwo = ""; var maxInput = 6000; if (testScript() == false) { return false; } if ((checkFormElement (theDocument.forms[0].elements[0]) == false) || (checkSequenceLength(theDocument.forms[0].elements[0].value, maxInput) == false) || (checkFormElement (theDocument.forms[0].elements[1]) == false) || (checkSequenceLength(theDocument.forms[0].elements[1].value, maxInput) == false)) { return false; } var MATRIX = "codon"; var BEGIN_GAP_PENALTY = parseInt(theDocument.forms[0].elements[5].options[theDocument.forms[0].elements[5].selectedIndex].value); var GAP_PENALTY = parseInt(theDocument.forms[0].elements[6].options[theDocument.forms[0].elements[6].selectedIndex].value); var END_GAP_PENALTY = parseInt(theDocument.forms[0].elements[7].options[theDocument.forms[0].elements[7].selectedIndex].value); // Removed some error checking // Replace u with t and U with T newCodonsOne = getSequenceFromFasta(theDocument.forms[0].elements[0].value); newCodonsOne = removeNonDna(newCodonsOne); newCodonsOne = newCodonsOne.replace(/u/g,"t"); newCodonsOne = newCodonsOne.replace(/U/g,"T"); newCodonsTwo = removeNonDnaStrict(newCodonsOne); titleOne = getTitleFromFasta(theDocument.forms[0].elements[0].value); newCodonsTwo = getSequenceFromFasta(theDocument.forms[0].elements[1].value); newCodonsTwo = removeNonDna(newCodonsTwo); newCodonsTwo = newCodonsTwo.replace(/u/gi,"t"); newCodonsTwo = newCodonsTwo.replace(/U/gi,"T"); newCodonsTwo = removeNonDnaStrict(newCodonsTwo); titleTwo = getTitleFromFasta(theDocument.forms[0].elements[1].value); // // Check if coding sequences are correct - divisible by if ((newCodonsOne.length % 3 != 0) || (newCodonsTwo.length % 3 != 0)) { alert(newCodonsOne.length); alert(newCodonsTwo); alert ("The sequences must be evenly divisible by 3. "); return false; } // Moved this after divisible by 3 error check openWindow("Pairwise Align Codons"); openPre(); outputWindow.document.write(getPairwiseAlignTitle(titleOne, newCodonsOne, titleTwo, newCodonsTwo)); //change to arrays for pass by reference, so that large sequence isn't copied // Added two .. to accomodate the codon length of 3 if (newCodonsOne.search(/.../) != -1) { newCodonsOne = newCodonsOne.match(/.../g); } if (newCodonsTwo.search(/.../) != -1) { newCodonsTwo = newCodonsTwo.match(/.../g); } pairwiseCodon (titleOne, newCodonsOne, titleTwo, newCodonsTwo, MATRIX, GAP_PENALTY, BEGIN_GAP_PENALTY, END_GAP_PENALTY); closePre(); closeWindow(); return true; } function pairwiseCodon (titleOne, newCodonsOne, titleTwo, newCodonsTwo, matrix, gapPenalty, beginGapPenalty, endGapPenalty) { //can use one or both. //can compare scores (should be identical) var useLinearSpace = true; var useQuadraticSpace = false; //create scoringMatrix object var scoringMatrix; scoringMatrix = new Codon(); var scoreSet = new ScoreSet(); scoreSet.setScoreSetParam(scoringMatrix, gapPenalty, beginGapPenalty, endGapPenalty); var alignment; if (useLinearSpace) { alignment = new AlignPairLinear(); alignment.setAlignParam(newCodonsOne, newCodonsTwo, scoreSet); alignment.align(); outputWindow.document.write(">" + titleOne + "\n"); outputWindow.document.write(addReturns(alignment.getAlignedM())); outputWindow.document.write("\n"); outputWindow.document.write("\n"); outputWindow.document.write(">" + titleTwo + "\n"); outputWindow.document.write(addReturns(alignment.getAlignedN())); outputWindow.document.write("\n\n"); outputWindow.document.write("Alignment score: " + alignment.score + "\n\n"); } if (useQuadraticSpace) { alignment = new AlignPairQuad(); alignment.initializeMatrix(newCodonsOne, newCodonsTwo, scoreSet); alignment.fillMatrix(); //alignment.dumpMatrix(); alignment.align(); outputWindow.document.write(">" + titleOne + "\n"); outputWindow.document.write(addReturns(alignment.getAlignedM())); outputWindow.document.write("\n"); outputWindow.document.write("\n"); outputWindow.document.write(">" + titleTwo + "\n"); outputWindow.document.write(addReturns(alignment.getAlignedN())); outputWindow.document.write("\n\n"); outputWindow.document.write("Alignment score: " + alignment.score + "\n\n"); } } //------------------------------------ ScoreSet class //ScoreSet getScore function getScore (r1, r2) { return this.scoringMatrix.scoringMatrix_getScore(r1, r2); } //ScoreSet setScoreSetParam function setScoreSetParam (scoringMatrix, gapPenalty, beginGapPenalty, endGapPenalty) { this.scoringMatrix = scoringMatrix; this.gap = gapPenalty; this.beginGap = beginGapPenalty; this.endGap = endGapPenalty; } //ScoreSet class function ScoreSet () { this.scoringMatrix; this.gap; this.beginGap; this.endGap; this.useBeginGapTop = true; this.useBeginGapLeft = true; this.useEndGapBottom = true; this.useEndGapRight = true; } //create and throw away a prototype object new ScoreSet(); //define object methods ScoreSet.prototype.getScore = getScore; ScoreSet.prototype.setScoreSetParam = setScoreSetParam; //------------------------------------ //------------------------------------ ScoringMatrix Abstract Class //ScoringMatrix getScore method function scoringMatrix_getScore(r1, r2) { r1 = r1.toLowerCase(); r2 = r2.toLowerCase(); if (this.scoreHash[r1 + r2] == null) { throw "Unrecognized residue pair: " + r1 + ", " + r2 + "."; } else { return this.scoreHash[r1 + r2]; } } function scoringMatrix_fillHash(matrix) { var cols = matrix[0].split(/\s+/); var cells; //go through rows for (var i = 1; i < matrix.length; i++) { cells = matrix[i].split(/\s+/); //go through cells in this row for (var j = 1; j < cols.length + 1; j++) { this.scoreHash[cells[0].toLowerCase() + cols[j-1].toLowerCase()] = parseInt(cells[j]); } } } //ScoringMatrix class function ScoringMatrix() { this.scoreHash = {}; } //create and throw away a prototype object new ScoringMatrix(); //define object methods ScoringMatrix.prototype.scoringMatrix_getScore = scoringMatrix_getScore; ScoringMatrix.prototype.scoringMatrix_fillHash = scoringMatrix_fillHash; //------------------------------------ Codon Class extends ScoringMatrix Class //constructor function Codon () { var matrix = new Array ( "AAA AAC AAG AAT ACA ACC ACG ACT AGA AGC AGG AGT ATA ATC ATG ATT CAA CAC CAG CAT CCA CCC CCG CCT CGA CGC CGG CGT CTA CTC CTG CTT GAA GAC GAG GAT GCA GCC GCG GCT GGA GGC GGG GGT GTA GTC GTG GTT TAA TAC TAG TAT TCA TCC TCG TCT TGA TGC TGG TGT TTA TTC TTG TTT", "AAA 11.6 -2.7 9.7 -1.7 -2.7 -6.4 -3.9 -5.6 5.1 -5.0 3.6 -4.2 -6.3 -13.0 -7.1 -11.5 0.4 -6.0 -1.9 -5.3 -8.5 -11.2 -8.9 -10.8 2.1 0.0 1.4 0.2 -10.2 -13.5 -13.0 -12.5 -2.6 -8.5 -5.0 -8.1 -6.3 -9.9 -7.5 -9.0 -7.1 -10.2 -8.2 -9.2 -8.2 -12.5 -11.1 -11.4 -50.0 -14.8 -50.0 -13.8 -7.3 -10.1 -8.4 -9.1 -50.0 -13.0 -13.5 -12.4 -10.7 -18.1 -11.8 -17.2", "AAC -2.7 13.0 -3.3 10.9 -3.5 -0.4 -3.3 -1.8 -5.4 4.6 -5.5 3.0 -10.2 -7.9 -9.9 -9.6 -5.0 0.5 -5.5 -1.0 -10.3 -8.1 -9.4 -9.6 -8.1 -5.0 -7.3 -6.3 -13.4 -11.3 -14.4 -12.9 -6.3 0.8 -6.4 -1.1 -7.4 -5.0 -6.2 -6.5 -5.6 -1.6 -4.7 -3.0 -10.8 -8.7 -11.9 -10.0 -50.0 -6.2 -50.0 -7.5 -6.3 -4.3 -6.2 -5.4 -50.0 -7.0 -16.3 -8.2 -13.2 -12.3 -13.1 -13.3", "AAG 9.7 -3.3 11.6 -2.8 -4.5 -6.7 -3.1 -6.9 3.3 -5.5 4.8 -5.1 -8.9 -13.2 -5.7 -12.6 -1.5 -6.1 -0.6 -6.1 -10.0 -11.8 -8.6 -11.9 1.2 0.5 2.2 0.1 -11.8 -14.0 -11.9 -13.4 -4.9 -9.1 -3.4 -8.9 -8.0 -10.0 -7.2 -10.0 -9.1 -10.2 -7.1 -9.9 -10.1 -13.0 -10.6 -12.7 -50.0 -14.9 -50.0 -14.4 -8.9 -10.8 -8.9 -10.4 -50.0 -13.1 -11.8 -13.0 -12.4 -19.4 -11.5 -17.8", "AAT -1.7 10.9 -2.8 12.9 -2.7 -2.2 -2.8 0.2 -4.8 2.9 -5.2 5.2 -9.1 -9.5 -9.0 -7.0 -4.0 -1.0 -5.0 1.0 -9.0 -8.8 -8.9 -7.7 -7.0 -6.8 -7.1 -4.3 -12.4 -12.9 -13.9 -10.0 -4.9 -0.7 -5.6 1.4 -6.0 -6.5 -6.2 -4.8 -5.1 -3.2 -5.0 -1.2 -9.8 -9.9 -11.3 -8.2 -50.0 -7.6 -50.0 -5.1 -5.5 -5.8 -5.9 -4.2 -50.0 -8.3 -15.5 -5.9 -11.6 -14.2 -12.0 -11.6", "ACA -2.7 -3.5 -4.5 -2.7 11.7 9.0 10.6 9.6 -3.2 -0.7 -5.1 -0.4 0.7 -4.6 -0.4 -3.6 -4.8 -8.9 -6.5 -7.8 -1.4 -4.1 -2.9 -3.3 -8.0 -9.1 -8.0 -8.2 -6.0 -9.3 -7.7 -8.5 -6.4 -10.1 -7.5 -8.6 2.8 -0.7 0.9 0.1 -5.9 -7.3 -6.5 -6.5 -0.4 -3.9 -2.6 -3.1 -50.0 -14.6 -50.0 -12.6 2.9 0.1 1.8 1.0 -50.0 -9.2 -13.6 -7.7 -4.8 -12.2 -6.2 -11.0", "ACC -6.4 -0.4 -6.7 -2.2 9.0 12.3 9.8 9.6 -7.1 2.4 -7.2 0.3 -2.9 -1.2 -3.0 -3.3 -7.6 -6.7 -8.1 -7.9 -4.9 -1.9 -4.5 -3.8 -9.5 -7.8 -9.3 -8.9 -9.4 -7.1 -9.0 -9.0 -9.4 -7.5 -9.3 -9.2 -0.7 2.6 0.2 -0.1 -8.0 -4.6 -7.7 -6.1 -3.6 -1.0 -4.1 -3.1 -50.0 -11.6 -50.0 -11.6 0.2 2.3 0.4 0.5 -50.0 -6.5 -15.3 -7.8 -8.4 -9.5 -8.3 -11.1", "ACG -3.9 -3.3 -3.1 -2.8 10.6 9.8 12.2 9.8 -4.9 0.1 -3.6 -0.2 -1.7 -4.1 0.9 -3.5 -5.9 -8.9 -5.6 -8.5 -3.9 -3.9 -2.2 -4.5 -7.3 -7.5 -6.4 -8.5 -7.1 -8.2 -6.7 -7.8 -7.9 -9.1 -7.1 -9.4 0.9 -0.2 2.5 -0.3 -6.9 -6.5 -5.5 -6.8 -1.7 -3.4 -1.7 -2.8 -50.0 -13.0 -50.0 -11.5 1.5 0.7 2.7 0.6 -50.0 -8.9 -12.1 -7.4 -6.1 -11.5 -5.4 -10.4", "ACT -5.6 -1.8 -6.9 0.2 9.6 9.6 9.8 11.6 -6.6 0.9 -7.2 2.5 -2.3 -3.4 -2.3 -0.6 -6.5 -8.2 -8.0 -6.3 -3.7 -3.5 -3.9 -1.6 -9.9 -8.9 -9.6 -7.0 -8.6 -8.9 -8.8 -6.8 -8.6 -8.2 -8.8 -6.8 0.3 0.1 0.2 2.4 -7.4 -6.2 -6.9 -4.4 -2.9 -2.9 -3.5 -0.9 -50.0 -12.2 -50.0 -10.1 1.2 0.6 1.2 2.4 -50.0 -7.6 -16.1 -5.8 -7.2 -10.8 -7.4 -9.0", "AGA 5.1 -5.4 3.3 -4.8 -3.2 -7.1 -4.9 -6.6 13.3 -2.8 11.2 -1.9 -5.7 -12.5 -7.2 -11.6 -0.7 -4.8 -3.1 -4.3 -10.0 -11.6 -8.8 -11.7 10.5 7.7 9.1 8.5 -9.8 -12.7 -11.7 -11.8 -6.3 -11.4 -8.8 -11.0 -7.5 -10.3 -8.3 -9.9 -1.9 -6.7 -4.1 -6.4 -7.9 -12.5 -11.4 -11.7 -50.0 -14.0 -50.0 -13.2 -8.5 -10.4 -9.1 -9.6 -50.0 -9.8 -7.7 -8.8 -10.3 -17.9 -11.8 -16.0", "AGC -5.0 4.6 -5.5 2.9 -0.7 2.4 0.1 0.9 -2.8 12.8 -2.6 11.0 -8.4 -6.3 -8.3 -7.7 -6.1 -2.9 -6.5 -4.2 -8.5 -5.9 -7.5 -7.7 -5.5 -2.4 -5.5 -4.1 -12.9 -10.3 -12.7 -11.3 -7.4 -3.1 -7.4 -4.9 -4.4 -1.8 -3.5 -3.5 -1.6 3.0 -0.8 0.9 -8.4 -6.3 -9.6 -7.3 -50.0 -9.0 -50.0 -9.7 -2.3 -0.2 -1.2 -1.5 -50.0 -0.7 -13.3 -2.0 -11.8 -11.9 -12.3 -12.7", "AGG 3.6 -5.5 4.8 -5.2 -5.1 -7.2 -3.6 -7.2 11.2 -2.6 13.4 -2.1 -7.7 -12.5 -5.3 -11.9 -2.2 -4.4 -1.9 -4.8 -10.2 -11.5 -8.1 -12.0 9.3 8.2 10.0 8.0 -10.8 -11.9 -10.7 -12.4 -8.2 -11.8 -6.9 -11.5 -8.4 -9.9 -7.1 -10.6 -4.7 -6.8 -1.2 -7.0 -9.8 -11.6 -9.6 -12.1 -50.0 -14.1 -50.0 -12.7 -10.0 -10.8 -8.8 -10.5 -50.0 -9.2 -4.2 -9.3 -11.0 -18.2 -11.1 -16.1", "AGT -4.2 3.0 -5.1 5.2 -0.4 0.3 -0.2 2.5 -1.9 11.0 -2.1 13.2 -7.6 -8.5 -8.0 -5.3 -5.6 -4.5 -6.8 -2.4 -7.8 -7.9 -7.9 -6.2 -5.7 -5.1 -5.4 -2.1 -12.4 -12.3 -13.1 -10.1 -6.6 -4.4 -6.9 -2.6 -3.6 -3.8 -3.7 -2.0 -1.4 0.8 -0.9 3.0 -8.2 -8.1 -9.2 -5.8 -50.0 -10.1 -50.0 -7.4 -1.7 -2.0 -1.5 -0.5 -50.0 -2.1 -12.6 -0.4 -11.6 -13.9 -11.4 -11.1", "ATA -6.3 -10.2 -8.9 -9.1 0.7 -2.9 -1.7 -2.3 -5.7 -8.4 -7.7 -7.6 13.2 9.6 3.5 9.7 -8.7 -12.4 -10.7 -10.7 -7.8 -10.2 -8.8 -9.6 -9.5 -11.9 -10.9 -10.5 2.3 -0.4 -0.2 -0.3 -9.7 -15.5 -11.4 -13.7 -3.0 -6.4 -4.1 -5.4 -9.6 -11.9 -10.5 -11.8 6.2 3.3 3.7 3.6 -50.0 -13.6 -50.0 -11.9 -5.6 -8.8 -7.2 -8.9 -50.0 -12.4 -14.1 -11.6 2.8 -6.4 0.5 -5.2", "ATC -13.0 -7.9 -13.2 -9.5 -4.6 -1.2 -4.1 -3.4 -12.5 -6.3 -12.5 -8.5 9.6 12.7 0.2 10.5 -12.4 -11.6 -13.2 -12.0 -12.4 -10.1 -11.6 -12.0 -15.1 -13.1 -14.3 -13.4 -1.4 1.4 -1.6 -0.5 -14.9 -14.3 -15.2 -16.8 -7.7 -4.7 -6.3 -6.6 -14.6 -10.8 -12.8 -13.0 2.3 6.0 2.5 3.6 -50.0 -11.2 -50.0 -11.9 -10.5 -9.2 -10.5 -10.5 -50.0 -10.3 -16.2 -11.3 -1.7 -3.7 -2.5 -5.4", "ATG -7.1 -9.9 -5.7 -9.0 -0.4 -3.0 0.9 -2.3 -7.2 -8.3 -5.3 -8.0 3.5 0.2 14.3 1.0 -7.3 -11.2 -6.9 -9.7 -8.5 -10.2 -7.7 -9.8 -10.0 -10.4 -8.4 -10.2 1.0 -0.6 1.7 -0.5 -11.1 -14.8 -9.7 -14.5 -3.7 -5.8 -3.1 -5.6 -10.4 -11.5 -8.2 -11.1 0.6 -1.6 1.6 -1.1 -50.0 -12.4 -50.0 -11.5 -5.5 -8.0 -4.9 -7.2 -50.0 -12.4 -10.3 -11.6 0.7 -6.8 2.4 -6.0", "ATT -11.5 -9.6 -12.6 -7.0 -3.6 -3.3 -3.5 -0.6 -11.6 -7.7 -11.9 -5.3 9.7 10.5 1.0 12.6 -12.0 -12.2 -12.5 -9.7 -11.1 -11.2 -11.9 -9.4 -12.9 -14.3 -14.0 -11.9 -1.0 -0.4 -1.6 1.2 -13.9 -15.4 -13.7 -12.6 -6.2 -6.7 -6.3 -4.4 -13.0 -12.2 -13.0 -10.4 2.9 3.8 2.5 5.8 -50.0 -12.5 -50.0 -10.2 -9.6 -9.7 -9.6 -8.3 -50.0 -11.6 -15.4 -9.4 -1.1 -5.4 -1.6 -3.3", "CAA 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