User:ChristopherW

From 2013.igem.org

(Difference between revisions)
 
(79 intermediate revisions not shown)
Line 1: Line 1:
<html>
<html>
<head>
<head>
-
<title>AutoAnnotator by Team TU-Munich 2013</title>
+
<script type="text/javascript" src="http://code.jquery.com/jquery-1.10.0.min.js"></script>
-
</head>
+
<script type="text/javascript" src="http://api.jquery.com/resources/events.js"></script>
-
<body>
+
-
<input type="button" onclick="myFunction()" value="Show alert box" />
+
 +
<script type="text/javascript" src="https://2013.igem.org/Team:TU-Munich/AjaxExtension.js?action=raw&ctype=text/js"></script>
 +
<script type="text/javascript" src="https://2013.igem.org/Team:TU-Munich/md5_pajhome.js?action=raw&ctype=text/js"></script>
 +
<script type="text/javascript" src="https://2013.igem.org/Team:TU-Munich/Flot.js?action=raw&ctype=text/js"></script>
-
<body>
+
<!-- IMPORTANT: DON'T REMOVE THIS LINE, OTHERWISE NOT SUPPORTED FOR IE BEFORE 9 -->
 +
<!--[if lte IE 8]><script language="javascript" type="text/javascript" src="excanvas.min.js"></script><![endif]-->
-
<p id="Command">Enter a sequence below!</p>
+
<script type="text/javascript" src="https://2013.igem.org/Team:TU-Munich/AnnotatorCode2.js?action=raw&ctype=text/js"></script>
-
<input type="text" id="EnteredSequence"> Enter sequence!
+
-
<br>
+
<title>AutoAnnotator by Team TU-Munich 2013</title>
-
<input type="button" onclick="go_countingFun()" value="Click here to create table">
+
-
<p id="CountingResult">Counting Array will appear here!</p>
+
-
<script>
+
</head>
-
function myFunction()
+
<body>
-
{
+
-
readSequence()
+
-
window.alert("Hello! I am an alert box!");
+
-
};
+
-
/**
+
<p id="Command">Enter a BioBrick number below, either starting with "BBa_" or just the alphanumeric code! <br>
-
*  DATA VALUES
+
Alternatively (e.g. for new BioBricks, which aren't in the Registry yet) you can enter the nucleotide sequence directly.
-
*/
+
</p>
-
var amino_acids = {A:0,R:0,N:0,D:0,C:0,Q:0,E:0,G:0,H:0,K:0,M:0,F:0,P:0,S:0,T:0,W:0,Y:0,V:0};
+
<form>
 +
<input type="text" id="EnteredBioBrick"> Enter BioBrick number or DNA sequence!
 +
<br>
 +
<input type="button" id="CreateTableButton" onclick="get_sequence()" value="Click here to create table">
 +
</form>
-
// IUPAC amino acid weights
+
<p id="htmlExplanation"></p>
-
var amino_weights = {
+
<p id="htmlTable"></p>
-
    "A":  89.09,
+
-
    "C": 121.16,
+
-
    "D": 133.10,
+
-
    "E": 147.13,
+
-
    "F": 165.19,
+
-
    "G":  75.07,
+
-
    "H": 155.16,
+
-
    "I": 131.18,
+
-
    "K": 146.19,
+
-
    "L": 131.18,
+
-
    "M": 149.21,
+
-
    "N": 132.12,
+
-
    "P": 115.13,
+
-
    "Q": 146.15,
+
-
    "R": 174.20,
+
-
    "S": 105.09,
+
-
    "T": 119.12,
+
-
    "V": 117.15,
+
-
    "W": 204.23,
+
-
    "Y": 181.19
+
-
    };
+
-
var water_weight = 18.02;
+
-
// Kyte & Doolittle index of hydrophobicity
+
<p id="wikiExplanation"></p>
-
var kd = {
+
-
  'A': 1.8, 'R':-4.5, 'N':-3.5, 'D':-3.5, 'C': 2.5,
+
-
      'Q':-3.5, 'E':-3.5, 'G':-0.4, 'H':-3.2, 'I': 4.5,
+
-
      'L': 3.8, 'K':-3.9, 'M': 1.9, 'F': 2.8, 'P':-1.6,
+
-
      'S':-0.8, 'T':-0.7, 'W':-0.9, 'Y':-1.3, 'V': 4.2 };
+
-
// Flexibility
+
<textarea readonly id="wikiTable" style="width:100%; display: none;" rows="4"></textarea>
-
// Normalized flexibility parameters (B-values), average (Vihinen et al., 1994)
+
-
var Flex= {
+
-
  'A': 0.984, 'C': 0.906, 'E': 1.094, 'D': 1.068,
+
-
      'G': 1.031, 'F': 0.915, 'I': 0.927, 'H': 0.950,
+
-
      'K': 1.102, 'M': 0.952, 'L': 0.935, 'N': 1.048,
+
-
      'Q': 1.037, 'P': 1.049, 'S': 1.046, 'R': 1.008,
+
-
      'T': 0.997, 'W': 0.904, 'V': 0.931, 'Y': 0.929};
+
-
// Hydrophilicity
+
<script>
-
// 1 Hopp & Wood
+
//for enter to trigger program when cursor in the textfield
-
// Proc. Natl. Acad. Sci. U.S.A. 78:3824-3828(1981).
+
$('#EnteredBioBrick').keyup(function(event) {
-
var hw = {
+
if (event.which == 13){
-
  'A':-0.5, 'R': 3.0, 'N': 0.2, 'D': 3.0, 'C':-1.0,
+
$('#EnteredBioBrick').blur(); //to loose focus
-
      'Q': 0.2, 'E': 3.0, 'G': 0.0, 'H':-0.5, 'I':-1.8,
+
$('#CreateTableButton').click();
-
      'L':-1.8, 'K': 3.0, 'M':-1.3, 'F':-2.5, 'P': 0.0,
+
-
      'S': 0.3, 'T':-0.4, 'W':-3.4, 'Y':-2.3, 'V':-1.5 };
+
-
 
+
-
// Surface accessibility
+
-
// 1 Emini Surface fractional probability
+
-
var em = {
+
-
  'A': 0.815, 'R': 1.475, 'N': 1.296, 'D': 1.283, 'C': 0.394,
+
-
      'Q': 1.348, 'E': 1.445, 'G': 0.714, 'H': 1.180, 'I': 0.603,
+
-
      'L': 0.603, 'K': 1.545, 'M': 0.714, 'F': 0.695, 'P': 1.236,
+
-
      'S': 1.115, 'T': 1.184, 'W': 0.808, 'Y': 1.089, 'V': 0.606 };
+
-
 
+
-
// 2 Janin Interior to surface transfer energy scale
+
-
var ja = {
+
-
  'A': 0.28, 'R':-1.14, 'N':-0.55, 'D':-0.52, 'C': 0.97,
+
-
      'Q':-0.69, 'E':-1.01, 'G': 0.43, 'H':-0.31, 'I': 0.60,
+
-
      'L': 0.60, 'K':-1.62, 'M': 0.43, 'F': 0.46, 'P':-0.42,
+
-
      'S':-0.19, 'T':-0.32, 'W': 0.29, 'Y':-0.15, 'V': 0.60 };
+
-
 
+
-
// A two dimentional dictionary for calculating the instability index.
+
-
// Guruprasad K., Reddy B.V.B., Pandit M.W.    Protein Engineering 4:155-161(1990).
+
-
// It is based on dipeptide values therefore the vale for the dipeptide DG is DIWV['D']['G'].
+
-
var DIWV = {
+
-
'A': {'A': 1.0, 'C': 44.94, 'E': 1.0, 'D': -7.49,
+
-
              'G': 1.0, 'F': 1.0, 'I': 1.0, 'H': -7.49,
+
-
              'K': 1.0, 'M': 1.0, 'L': 1.0, 'N': 1.0,
+
-
              'Q': 1.0, 'P': 20.26, 'S': 1.0, 'R': 1.0,
+
-
              'T': 1.0, 'W': 1.0, 'V': 1.0, 'Y': 1.0 },
+
-
        'C': {'A': 1.0, 'C': 1.0, 'E': 1.0, 'D': 20.26,
+
-
              'G': 1.0, 'F': 1.0, 'I': 1.0, 'H': 33.60,
+
-
              'K': 1.0, 'M': 33.60, 'L': 20.26, 'N': 1.0,
+
-
              'Q': -6.54, 'P': 20.26, 'S': 1.0, 'R': 1.0,
+
-
              'T': 33.60, 'W': 24.68, 'V': -6.54, 'Y': 1.0},
+
-
        'E': {'A': 1.0, 'C': 44.94, 'E': 33.60, 'D': 20.26,
+
-
              'G': 1.0, 'F': 1.0, 'I': 20.26, 'H': -6.54,
+
-
              'K': 1.0, 'M': 1.0, 'L': 1.0, 'N': 1.0,
+
-
              'Q': 20.26, 'P': 20.26, 'S': 20.26, 'R': 1.0,
+
-
              'T': 1.0, 'W': -14.03, 'V': 1.0, 'Y': 1.0},
+
-
        'D': {'A': 1.0, 'C': 1.0, 'E': 1.0, 'D': 1.0,
+
-
              'G': 1.0, 'F': -6.54, 'I': 1.0, 'H': 1.0,
+
-
              'K': -7.49, 'M': 1.0, 'L': 1.0, 'N': 1.0,
+
-
              'Q': 1.0, 'P': 1.0, 'S': 20.26, 'R': -6.54,
+
-
              'T': -14.03, 'W': 1.0, 'V': 1.0, 'Y': 1.0},
+
-
        'G': {'A': -7.49, 'C': 1.0, 'E': -6.54, 'D': 1.0,
+
-
              'G': 13.34, 'F': 1.0, 'I': -7.49, 'H': 1.0,
+
-
              'K': -7.49, 'M': 1.0, 'L': 1.0, 'N': -7.49,
+
-
              'Q': 1.0, 'P': 1.0, 'S': 1.0, 'R': 1.0,
+
-
              'T': -7.49, 'W': 13.34, 'V': 1.0, 'Y': -7.49},
+
-
        'F': {'A': 1.0, 'C': 1.0, 'E': 1.0, 'D': 13.34,
+
-
              'G': 1.0, 'F': 1.0, 'I': 1.0, 'H': 1.0,
+
-
              'K': -14.03, 'M': 1.0, 'L': 1.0, 'N': 1.0,
+
-
              'Q': 1.0, 'P': 20.26, 'S': 1.0, 'R': 1.0,
+
-
              'T': 1.0, 'W': 1.0, 'V': 1.0, 'Y': 33.601},
+
-
        'I': {'A': 1.0, 'C': 1.0, 'E': 44.94, 'D': 1.0,
+
-
              'G': 1.0, 'F': 1.0, 'I': 1.0, 'H': 13.34,
+
-
              'K': -7.49, 'M': 1.0, 'L': 20.26, 'N': 1.0,
+
-
              'Q': 1.0, 'P': -1.88, 'S': 1.0, 'R': 1.0,
+
-
              'T': 1.0, 'W': 1.0, 'V': -7.49, 'Y': 1.0},
+
-
        'H': {'A': 1.0, 'C': 1.0, 'E': 1.0, 'D': 1.0,
+
-
              'G': -9.37, 'F': -9.37, 'I': 44.94, 'H': 1.0,
+
-
              'K': 24.68, 'M': 1.0, 'L': 1.0, 'N': 24.68,
+
-
              'Q': 1.0, 'P': -1.88, 'S': 1.0, 'R': 1.0,
+
-
              'T': -6.54, 'W': -1.88, 'V': 1.0, 'Y': 44.94},
+
-
        'K': {'A': 1.0, 'C': 1.0, 'E': 1.0, 'D': 1.0,
+
-
              'G': -7.49, 'F': 1.0, 'I': -7.49, 'H': 1.0,
+
-
              'K': 1.0, 'M': 33.60, 'L': -7.49, 'N': 1.0,
+
-
              'Q': 24.64, 'P': -6.54, 'S': 1.0, 'R': 33.60,
+
-
              'T': 1.0, 'W': 1.0, 'V': -7.49, 'Y': 1.0},
+
-
        'M': {'A': 13.34, 'C': 1.0, 'E': 1.0, 'D': 1.0,
+
-
              'G': 1.0, 'F': 1.0, 'I': 1.0, 'H': 58.28,
+
-
              'K': 1.0, 'M': -1.88, 'L': 1.0, 'N': 1.0,
+
-
              'Q': -6.54, 'P': 44.94, 'S': 44.94, 'R': -6.54,
+
-
              'T': -1.88, 'W': 1.0, 'V': 1.0, 'Y': 24.68},
+
-
        'L': {'A': 1.0, 'C': 1.0, 'E': 1.0, 'D': 1.0,
+
-
              'G': 1.0, 'F': 1.0, 'I': 1.0, 'H': 1.0,
+
-
              'K': -7.49, 'M': 1.0, 'L': 1.0, 'N': 1.0,
+
-
              'Q': 33.60, 'P': 20.26, 'S': 1.0, 'R': 20.26,
+
-
              'T': 1.0, 'W': 24.68, 'V': 1.0, 'Y': 1.0},
+
-
        'N': {'A': 1.0, 'C': -1.88, 'E': 1.0, 'D': 1.0,
+
-
              'G': -14.03, 'F': -14.03, 'I': 44.94, 'H': 1.0,
+
-
              'K': 24.68, 'M': 1.0, 'L': 1.0, 'N': 1.0,
+
-
              'Q': -6.54, 'P': -1.88, 'S': 1.0, 'R': 1.0,
+
-
              'T': -7.49, 'W': -9.37, 'V': 1.0, 'Y': 1.0},
+
-
        'Q': {'A': 1.0, 'C': -6.54, 'E': 20.26, 'D': 20.26,
+
-
              'G': 1.0, 'F': -6.54, 'I': 1.0, 'H': 1.0,
+
-
              'K': 1.0, 'M': 1.0, 'L': 1.0, 'N': 1.0,
+
-
              'Q': 20.26, 'P': 20.26, 'S': 44.94, 'R': 1.0,
+
-
              'T': 1.0, 'W': 1.0, 'V': -6.54, 'Y': -6.54},
+
-
        'P': {'A': 20.26, 'C': -6.54, 'E': 18.38, 'D': -6.54,
+
-
              'G': 1.0, 'F': 20.26, 'I': 1.0, 'H': 1.0,
+
-
              'K': 1.0, 'M': -6.54, 'L': 1.0, 'N': 1.0,
+
-
              'Q': 20.26, 'P': 20.26, 'S': 20.26, 'R': -6.54,
+
-
              'T': 1.0, 'W': -1.88, 'V': 20.26, 'Y': 1.0},
+
-
        'S': {'A': 1.0, 'C': 33.60, 'E': 20.26, 'D': 1.0,
+
-
              'G': 1.0, 'F': 1.0, 'I': 1.0, 'H': 1.0,
+
-
              'K': 1.0, 'M': 1.0, 'L': 1.0, 'N': 1.0,
+
-
              'Q': 20.26, 'P': 44.94, 'S': 20.26, 'R': 20.26,
+
-
              'T': 1.0, 'W': 1.0, 'V': 1.0, 'Y': 1.0},
+
-
        'R': {'A': 1.0, 'C': 1.0, 'E': 1.0, 'D': 1.0,
+
-
              'G': -7.49, 'F': 1.0, 'I': 1.0, 'H': 20.26,
+
-
              'K': 1.0, 'M': 1.0, 'L': 1.0, 'N': 13.34,
+
-
              'Q': 20.26, 'P': 20.26, 'S': 44.94, 'R': 58.28,
+
-
              'T': 1.0, 'W': 58.28, 'V': 1.0, 'Y': -6.54},
+
-
        'T': {'A': 1.0, 'C': 1.0, 'E': 20.26, 'D': 1.0,
+
-
              'G': -7.49, 'F': 13.34, 'I': 1.0, 'H': 1.0,
+
-
              'K': 1.0, 'M': 1.0, 'L': 1.0, 'N': -14.03,
+
-
              'Q': -6.54, 'P': 1.0, 'S': 1.0, 'R': 1.0,
+
-
              'T': 1.0, 'W': -14.03, 'V': 1.0, 'Y': 1.0},
+
-
        'W': {'A': -14.03, 'C': 1.0, 'E': 1.0, 'D': 1.0,
+
-
              'G': -9.37, 'F': 1.0, 'I': 1.0, 'H': 24.68,
+
-
              'K': 1.0, 'M': 24.68, 'L': 13.34, 'N': 13.34,
+
-
              'Q': 1.0, 'P': 1.0, 'S': 1.0, 'R': 1.0,
+
-
              'T': -14.03, 'W': 1.0, 'V': -7.49, 'Y': 1.0},
+
-
        'V': {'A': 1.0, 'C': 1.0, 'E': 1.0, 'D': -14.03,
+
-
              'G': -7.49, 'F': 1.0, 'I': 1.0, 'H': 1.0,
+
-
              'K': -1.88, 'M': 1.0, 'L': 1.0, 'N': 1.0,
+
-
              'Q': 1.0, 'P': 20.26, 'S': 1.0, 'R': 1.0,
+
-
              'T': -7.49, 'W': 1.0, 'V': 1.0, 'Y': -6.54},
+
-
        'Y': {'A': 24.68, 'C': 1.0, 'E': -6.54, 'D': 24.68,
+
-
              'G': -7.49, 'F': 1.0, 'I': 1.0, 'H': 13.34,
+
-
              'K': 1.0, 'M': 44.94, 'L': 1.0, 'N': 1.0,
+
-
              'Q': 1.0, 'P': 13.34, 'S': 1.0, 'R': -15.91,
+
-
              'T': -7.49, 'W': -9.37, 'V': 1.0, 'Y': 13.34}
+
-
        };
+
-
 
+
-
// Data for the calculation of the Isoelectric Point
+
-
/* pK values are from:
+
-
* Bjellqvist, B.,Hughes, G.J., Pasquali, Ch., Paquet, N., Ravier, F., Sanchez,
+
-
J.-Ch., Frutiger, S. & Hochstrasser, D.F.
+
-
The focusing positions of polypeptides in immobilized pH gradients can be predicted
+
-
from their amino acid sequences. Electrophoresis 1993, 14, 1023-1031.
+
-
* Bjellqvist, B., Basse, B., Olsen, E. and Celis, J.E.
+
-
Reference points for comparisons of two-dimensional maps of proteins from
+
-
different human cell types defined in a pH scale where isoelectric points correlate
+
-
with polypeptide compositions. Electrophoresis 1994, 15, 529-539.
+
-
*/
+
-
var positive_pKs = {'Nterm': 7.5 , 'K': 10.0, 'R': 12.0, 'H': 5.98          };
+
-
var negative_pKs = {'Cterm': 3.55, 'D': 4.05, 'E': 4.45, 'C': 9.0 , 'Y': 10.0};
+
-
var pKcterminal = {'D': 4.55, 'E': 4.75};
+
-
var pKnterminal = {'A': 7.59, 'M': 7.0, 'S': 6.93, 'P': 8.36, 'T': 6.82, 'V': 7.44, 'E': 7.7};
+
-
var charged_aas = ['K', 'R', 'H', 'D', 'E', 'C', 'Y'];
+
-
// or ProMost?
+
-
 
+
-
 
+
-
/**
+
-
*  FUNCTIONS
+
-
*/
+
-
 
+
-
function readSequence() {
+
-
var sequence = document.getElementById("EnteredSequence").value;
+
-
var cleanSequence = sequence.replace(/ /g, "");
+
-
return cleanSequence;
+
-
};
+
-
 
+
-
function count_amino_acids(sequence){
+
-
    //Counts standard amino acids, returns an array {AminoAcid:Number}
+
-
var amino_acids_content = {A:0,R:0,N:0,D:0,C:0,Q:0,E:0,G:0,H:0,K:0,M:0,F:0,P:0,S:0,T:0,W:0,Y:0,V:0};
+
-
var amino_acids_freq = {A:0,R:0,N:0,D:0,C:0,Q:0,E:0,G:0,H:0,K:0,M:0,F:0,P:0,S:0,T:0,W:0,Y:0,V:0};
+
-
for (i=0; i<sequence.length; i++){
+
-
amino_acids_content[sequence[i]]++;
+
}
}
-
var total=sequence.length;
+
})
-
for (aa in amino_acids){
+
$('#EnteredBioBrick').keydown(function(event) {
-
amino_acids_freq[aa] = amino_acids_content[aa] * (100 / total);
+
if (event.which == 13) {
-
};
+
  event.preventDefault();
-
return [amino_acids_content,amino_acids_freq];
+
-
};
+
-
 
+
-
function compute_molecular_weight(amino_acids_content){
+
-
var molec_weight = water_weight;
+
-
for (aa in amino_acids){
+
-
molec_weight = molec_weight + amino_acids_content[aa] * (amino_weights[aa] - water_weight);
+
-
}
+
-
return molec_weight;
+
}
}
-
 
+
});
-
function findReadingFrame(sequence){
+
-
var a = 0;
+
-
return a;
+
-
}
+
-
 
+
-
 
+
-
function go_countingFun() {
+
-
var input = readSequence();
+
-
var counting_result = count_amino_acids(input);
+
-
var amino_content = counting_result[0];
+
-
var amino_freq = counting_result[1];
+
-
var total_aminos = input.length;
+
-
var molecular_weight = compute_molecular_weight(amino_content);
+
-
// Create the output
+
-
var outputText = "" // + "You entered the sequence: "+input + "<br>The content is:<br>";
+
-
/* for (aa in amino_acids) {
+
-
outputText = outputText + " " +aa +" "+ amino_content[aa] + " "
+
-
+ amino_freq[aa].toFixed(2) + "%" + "<br>";
+
-
};
+
-
outputText = outputText + "The total number of amino acids is "
+
-
+ total_aminos + "<br><br>"
+
-
*/
+
-
outputText = outputText + "Copy the following into the wiki to get the protein-data-table: <br><br>"
+
-
+ "{|cellspacing=\"0\" border=\"1\" "
+
-
+ "<br>|colspan=\"20\"|'''Automatically determined parameters using the [http://www.mediawiki.org/wiki/Table BioBrick-AutoAnnotator]'''"
+
-
+ "<br>|-"
+
-
+ "<br>|colspan=\"10\"|BioBrick: <partinfo>BBa_K1159000</partinfo>"
+
-
+ "<br>|colspan=\"10\"|Used open reading frame from position ?x? to ?y?."
+
-
+ "<br>|-"
+
-
+ "<br>|A (Ala)"
+
-
+ "<br>|" + amino_content.A + " (" + amino_freq.A.toFixed(2) + "%)"
+
-
+ "<br>|R (Arg)"
+
-
+ "<br>|" + amino_content.R + " (" + amino_freq.R.toFixed(2) + "%)"
+
-
+ "<br>|N (Asn)"
+
-
+ "<br>|" + amino_content.N + " (" + amino_freq.N.toFixed(2) + "%)"
+
-
+ "<br>|D (Asp)"
+
-
+ "<br>|" + amino_content.D + " (" + amino_freq.D.toFixed(2) + "%)"
+
-
+ "<br>|C (Cys)"
+
-
+ "<br>|" + amino_content.C + " (" + amino_freq.C.toFixed(2) + "%)"
+
-
+ "<br>|Q (Gln)"
+
-
+ "<br>|" + amino_content.Q + " (" + amino_freq.Q.toFixed(2) + "%)"
+
-
+ "<br>|E (Glu)"
+
-
+ "<br>|" + amino_content.E + " (" + amino_freq.E.toFixed(2) + "%)"
+
-
+ "<br>|G (Gly)"
+
-
+ "<br>|" + amino_content.G + " (" + amino_freq.G.toFixed(2) + "%)"
+
-
+ "<br>|H (His)"
+
-
+ "<br>|" + amino_content.H + " (" + amino_freq.H.toFixed(2) + "%)"
+
-
+ "<br>|-"
+
-
+ "<br>|K (Lys):"
+
-
+ "<br>|" + amino_content.K + " (" + amino_freq.K.toFixed(2) + "%)"
+
-
+ "<br>|M (Met)"
+
-
+ "<br>|" + amino_content.M + " (" + amino_freq.M.toFixed(2) + "%)"
+
-
+ "<br>|F (Phe)"
+
-
+ "<br>|" + amino_content.F + " (" + amino_freq.F.toFixed(2) + "%)"
+
-
+ "<br>|P (Pro)"
+
-
+ "<br>|" + amino_content.P + " (" + amino_freq.P.toFixed(2) + "%)"
+
-
+ "<br>|S (Ser)"
+
-
+ "<br>|" + amino_content.S + " (" + amino_freq.S.toFixed(2) + "%)"
+
-
+ "<br>|T (Thr)"
+
-
+ "<br>|" + amino_content.T + " (" + amino_freq.T.toFixed(2) + "%)"
+
-
+ "<br>|W (Trp)"
+
-
+ "<br>|" + amino_content.W + " (" + amino_freq.W.toFixed(2) + "%)"
+
-
+ "<br>|Y (Tyr)"
+
-
+ "<br>|" + amino_content.Y + " (" + amino_freq.Y.toFixed(2) + "%)"
+
-
+ "<br>|V (Val)"
+
-
+ "<br>|" + amino_content.V + " (" + amino_freq.V.toFixed(2) + "%)"
+
-
+ "<br>|-"
+
-
+ "<br>|colspan=\"3\"|'''Amino acid counting:'''"
+
-
+ "<br>|colspan=\"3\"|Total number of amino acids (aa):"
+
-
+ "<br>|colspan=\"2\"|" + total_aminos
+
-
+ "<br>|colspan=\"3\"|Number of positively charged aa:"
+
-
+ "<br>|colspan=\"2\"|?9?"
+
-
+ "<br>|colspan=\"3\"|Number of negatively charged aa:"
+
-
+ "<br>|colspan=\"2\"|?9?"
+
-
+ "<br>|-"
+
-
+ "<br>|colspan=\"3\"|'''Biochemical parameters:'''"
+
-
+ "<br>|colspan=\"3\"|Molecular weight [Da]:"
+
-
+ "<br>|colspan=\"2\"|" + molecular_weight
+
-
+ "<br>|colspan=\"3\"|Theoretical pI:"
+
-
+ "<br>|colspan=\"2\"|?4?"
+
-
+ "<br>|colspan=\"3\"|Extinction coefficient:"
+
-
+ "<br>|colspan=\"2\"|?4?"
+
-
+ "<br>|-"
+
-
+ "<br>|colspan=\"3\"|'''Estimated half-life:'''"
+
-
+ "<br>|colspan=\"3\"|Mammals:"
+
-
+ "<br>|colspan=\"2\"|?4 h?"
+
-
+ "<br>|colspan=\"3\"|Yeast:"
+
-
+ "<br>|colspan=\"2\"|?4?"
+
-
+ "<br>|colspan=\"3\"|''E. coli'':"
+
-
+ "<br>|colspan=\"2\"|?4?"
+
-
+ "<br>|-"
+
-
+ "<br>|colspan=\"3\"|'''Codon usage:'''"
+
-
+ "<br>|colspan=\"3\"|Mammals:"
+
-
+ "<br>|colspan=\"2\"|?good?"
+
-
+ "<br>|colspan=\"3\"|Yeast:"
+
-
+ "<br>|colspan=\"2\"|?Ok?"
+
-
+ "<br>|colspan=\"3\"|''E. coli'':"
+
-
+ "<br>|colspan=\"2\"|?bad ?"
+
-
+ "<br>|-"
+
-
+ "<br>|colspan=\"3\"|'''RFC standard:'''"
+
-
+ "<br>|colspan=\"17\"|This is a RFC 25 BioBrick, thus ATGGCCGGC and ACCGGT were added to the 5' and 3' ends."
+
-
+ "<br>|-"
+
-
+ "<br>|colspan=\"20\"| The BioBrick-AutoAnnotator was created by [https://2013.igem.org/Team:TU-Munich TU-Munich 2013] iGEM team. For information please read the [https://2013.igem.org/Team:TU-Munich/Results/Software description]."
+
-
+ "<br>|}"
+
-
+ "<br><br>";
+
-
//document.write(outputText);
+
-
        document.getElementById("newoutput").innerHTML = outputText;
+
-
};
+
</script>
</script>
-
 
+
-
 
+
</body>
</body>
</html>
</html>
-
 
-
=Test=
 
-
 
-
 
-
 
-
{|cellspacing="0" border="1"
 
-
|colspan="20"|'''Automatically determined parameters using the [http://www.mediawiki.org/wiki/Table BioBrick-AutoAnnotator]'''
 
-
|-
 
-
|colspan="10"|BioBrick: BBa_K1159000
 
-
|colspan="10"|Used open reading frame from position ?x? to ?y?.
 
-
|-
 
-
|A (Ala)
 
-
|10 (4.00%)
 
-
|R (Arg)
 
-
|8 (3.20%)
 
-
|N (Asn)
 
-
|13 (5.20%)
 
-
|D (Asp)
 
-
|18 (7.20%)
 
-
|C (Cys)
 
-
|2 (0.80%)
 
-
|Q (Gln)
 
-
|8 (3.20%)
 
-
|E (Glu)
 
-
|16 (6.40%)
 
-
|G (Gly)
 
-
|25 (10.00%)
 
-
|H (His)
 
-
|10 (4.00%)
 
-
|-
 
-
|K (Lys):
 
-
|20 (8.00%)
 
-
|M (Met)
 
-
|6 (2.40%)
 
-
|F (Phe)
 
-
|13 (5.20%)
 
-
|P (Pro)
 
-
|11 (4.40%)
 
-
|S (Ser)
 
-
|9 (3.60%)
 
-
|T (Thr)
 
-
|16 (6.40%)
 
-
|W (Trp)
 
-
|1 (0.40%)
 
-
|Y (Tyr)
 
-
|12 (4.80%)
 
-
|V (Val)
 
-
|17 (6.80%)
 
-
|-
 
-
|colspan="3"|'''Amino acid counting:'''
 
-
|colspan="3"|Total number of amino acids (aa):
 
-
|colspan="2"|250
 
-
|colspan="3"|Number of positively charged aa:
 
-
|colspan="2"|?9?
 
-
|colspan="3"|Number of negatively charged aa:
 
-
|colspan="2"|?9?
 
-
|-
 
-
|colspan="3"|'''Biochemical parameters:'''
 
-
|colspan="3"|Molecular weight [Da]:
 
-
|colspan="2"|24190.279999999995
 
-
|colspan="3"|Theoretical pI:
 
-
|colspan="2"|?4?
 
-
|colspan="3"|Extinction coefficient:
 
-
|colspan="2"|?4?
 
-
|-
 
-
|colspan="3"|'''Estimated half-life:'''
 
-
|colspan="3"|Mammals:
 
-
|colspan="2"|?4 h?
 
-
|colspan="3"|Yeast:
 
-
|colspan="2"|?4?
 
-
|colspan="3"|''E. coli'':
 
-
|colspan="2"|?4?
 
-
|-
 
-
|colspan="3"|'''Codon usage:'''
 
-
|colspan="3"|Mammals:
 
-
|colspan="2"|?good?
 
-
|colspan="3"|Yeast:
 
-
|colspan="2"|?Ok?
 
-
|colspan="3"|''E. coli'':
 
-
|colspan="2"|?bad ?
 
-
|-
 
-
|colspan="3"|'''RFC standard:'''
 
-
|colspan="17"|This is a RFC 25 BioBrick, thus ATGGCCGGC and ACCGGT were added to the 5' and 3' ends.
 
-
|-
 
-
|colspan="20"| The BioBrick-AutoAnnotator was created by [https://2013.igem.org/Team:TU-Munich TU-Munich 2013] iGEM team. For information please read the [https://2013.igem.org/Team:TU-Munich/Results/Software description].
 
-
|}
 
-
<pre id="newoutput"></pre>
 

Latest revision as of 21:26, 14 September 2013

AutoAnnotator by Team TU-Munich 2013

Enter a BioBrick number below, either starting with "BBa_" or just the alphanumeric code!
Alternatively (e.g. for new BioBricks, which aren't in the Registry yet) you can enter the nucleotide sequence directly.

Enter BioBrick number or DNA sequence!

Retrieved from "http://2013.igem.org/User:ChristopherW"