Talk:Team:HokkaidoU Japan/Shuffling Kit/Primer Designer

<html>
  <head>
    <script src="http://code.jquery.com/jquery-1.10.1.min.js"></script>
    <script>
(function() {
  var calculate_tm, decide_annealing_site, delta_h, delta_s, main, sigma_delta_h, sigma_delta_s;

  delta_h = function(seq) {
    switch (seq) {
      case 'AA':
      case 'TT':
        return -9.1;
      case 'AT':
        return -8.6;
      case 'TA':
        return -6;
      case 'CA':
      case 'TG':
        return -5.8;
      case 'GT':
      case 'AC':
        return -6.5;
      case 'CT':
      case 'AG':
        return -7.8;
      case 'GA':
      case 'TC':
        return -5.6;
      case 'CG':
        return -11.9;
      case 'GC':
        return -11.1;
      case 'GG':
      case 'CC':
        return -11;
    }
  };

  sigma_delta_h = function(seq) {
    var i, sum, _i, _ref;
    sum = 0;
    for (i = _i = 0, _ref = seq.length - 2; 0 <= _ref ? _i <= _ref : _i >= _ref; i = 0 <= _ref ? ++_i : --_i) {
      sum += delta_h(seq.slice(i, +(i + 1) + 1 || 9e9));
    }
    return sum;
  };

  delta_s = function(seq) {
    switch (seq) {
      case 'AA':
      case 'TT':
        return -24;
      case 'AT':
        return -23.9;
      case 'TA':
        return -16.9;
      case 'CA':
      case 'TG':
        return -12.9;
      case 'GT':
      case 'AC':
        return -17.3;
      case 'CT':
      case 'AG':
        return -20.8;
      case 'GA':
      case 'TC':
        return -13.5;
      case 'CG':
        return -27.8;
      case 'GC':
        return -26.7;
      case 'GG':
      case 'CC':
        return -26.6;
    }
  };

  sigma_delta_s = function(seq) {
    var i, sum, _i, _ref;
    sum = 0;
    for (i = _i = 0, _ref = seq.length - 2; 0 <= _ref ? _i <= _ref : _i >= _ref; i = 0 <= _ref ? ++_i : --_i) {
      sum += delta_s(seq.slice(i, +(i + 1) + 1 || 9e9));
    }
    return sum;
  };

  calculate_tm = function(seq) {
    var h, s;
    h = sigma_delta_h(seq);
    s = sigma_delta_s(seq);
    return (1000 * h / (-10.8 + s + 1.987 * -15.89495209964411)) - 273.15 + 16.6 * -1.3010299956639813;
  };

  decide_annealing_site = function(seq) {
    var n, tm, _i;
    if (calculate_tm(seq.slice(0, 35)) < 60) {
      alert("Sequence is too short.");
    }
    for (n = _i = 17; _i <= 35; n = ++_i) {
      tm = calculate_tm(seq.slice(0, +(n - 1) + 1 || 9e9));
      if (tm > 60 && (seq[n - 1] === 'G' || seq[n - 1] === 'C')) {
        break;
      }
    }
    return [seq.slice(0, +(n - 1) + 1 || 9e9), tm];
  };

  main = function(over_f, over_r, seq) {
    var anneal_f, anneal_r, primer_f, primer_r, tm_f, tm_r;
    anneal_f = decide_annealing_site(seq);
    anneal_r = decide_annealing_site(seq.split("").reverse().join(""));
    primer_f = "TTTGGTCTCT" + over_f + "T" + anneal_f[0];
    tm_f = anneal_f[1];
    primer_r = "TTTGGTCTCA" + over_f + "A" + anneal_r[0];
    tm_r = anneal_r[1];
    return [primer_f, tm_f, primer_r, tm_r];
  };

  $(function() {
    return $('#primer-designer').submit(function(e) {
      var $button, $form, overhang_f, overhang_r, result, sequence;
      e.preventDefault();
      $form = $(this);
      $button = $form.find('button');
      $button.attr('disabled', true);
      overhang_f = $form.find('[name="overhang-f"]').val().toUpperCase();
      overhang_r = $form.find('[name="overhang-r"]').val().toUpperCase();
      sequence = $form.find('[name="sequence"]').val().toUpperCase();
      result = main(overhang_f, overhang_r, sequence);
      $('#primer-f').text(result[0]);
      $('#tm-f').text(result[1]);
      $('#primer-r').text(result[2]);
      $('#tm-r').text(result[3]);
      return $button.attr('disabled', false);
    });
  });

}).call(this);

    </script>
  </head>

  <body>
    <form id="primer-designer">
      Overhang_F <input type="text" name="overhang-f"><br>
      Overhang_R <input type="text" name="overhang-r"><br>
      Sequence <input type="text" name="sequence"><br>
      <button>Calculate</button>
    </form>

    <hr>

    <h4>Forward</h4>
    <dl>
      <dt>sequence</dt>
      <dd><pre id="primer-f"></pre></dd>
      <dt>tm</dt>
      <dd><pre id="tm-f"></pre></dd>
    </dl>
    <h4>Reverse</h4>
    <dl>
      <dt>sequence</dt>
      <dd><pre id="primer-r"></pre></dd>
      <dt>tm</dt>
      <dd><pre id="tm-r"></pre></dd>
    </dl>
  </body>
</html>