Team:Harvard/ZF Binding Site Finder

From 2011.igem.org

(Difference between revisions)
Line 1: Line 1:
 +
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<head>
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</style>
</style>
 +
<script type="text/javascript" src="http://ajax.googleapis.com/ajax/libs/jquery/1.4.2/jquery.min.js"></script>
<script type="text/javascript">
<script type="text/javascript">
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}
}
 +
 +
$.validator.addMethod(
 +
        "ntpCheck",
 +
        function(value, element, regexp) {
 +
            var re = new RegExp(regexp);
 +
            return this.optional(element) || re.test(value);
 +
        },
 +
        "You must enter a valid sequence of nine nucleotides containing G,T,C,A, or N."
 +
);
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//get zinc finger arrays for searching
//get zinc finger arrays for searching
-
var bottomzf = $("#bottom").val().toUpperCase();
+
var bottomzf = $("#bottominput").val().toUpperCase();
-
var topzf = $("#topsearch").val().toUpperCase();
+
var topzf = $("#topinput").val().toUpperCase();
-
 
+
-
//transform bottom zf to reverse complement
+
-
bottomzf = reverseComplement(bottomzf);
+
var ntpCheck = /[GCTAN]{9}/;
var ntpCheck = /[GCTAN]{9}/;
-
        alert(bottomzf.match(ntpCheck) && topzf.match(ntpCheck));
+
$("#results").html("what's up!");
-
 
+
/*
-
/* if (!(bottomzf.match(ntpCheck)&&
+
if (!(bottomzf.match(ntpCheck)&&
  topzf.match(ntpCheck)&&
  topzf.match(ntpCheck)&&
  (bottomzf.length=="9")&&
  (bottomzf.length=="9")&&
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}
}
*/
*/
 +
 +
$("#bottominput #topinput").rules("add", { regex: "[GCTAN]{9}" })
 +
 +
//transform bottom zf to reverse complement
 +
bottomzf = reverseComplement(bottomzf);
 +
 +
alert(bottomzf);
 +
alert(topzf);
 +
 +
 +
/*
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//start building regular expression from ZF fingers
 +
var siteExp = "(" + bottomzf.replace(/n/gi,"\\w");
 +
 +
//add in x NTPs between first and second finger
 +
var nucgap = document.getElementById("gap").value;
 +
for(i=0;i<nucgap;i++){
 +
siteExp = siteExp + "\\w";
 +
}
 +
 +
//finish building regular expression
 +
siteExp = siteExp + topzf.replace(/n/gi,"\\w") + "){1}";
 +
 +
//construct regular expression and find all instances of desired sequence in the test sequence
 +
var array1 = new RegExp(siteExp, "gi");
 +
var array2 = testseq.match(array1);
 +
 +
//error message if no sequences found
 +
if(testseq.search(array1) == -1)
 +
{
 +
document.getElementById("results").innerHTML = "No results found.";
 +
//if results are found, build table to display results
 +
} else {
 +
 +
var revComp = "";
 +
var seqtwo = "";
 +
 +
table = "<table><tr><td colspan='4'><b>Zinc Finger Binding Site Candidates</b></td></tr><td><b>Location</b></td><td><b>Bottom Sequence</b></td><td><b>Top Sequence</b></td><td><b>Entire Sequence (top strand perspective)</b></td>";
 +
 +
for(i=0;i<array2.length;i++)
 +
{
 +
array1.test(testseq);
 +
 +
table = table + "<tr>";
 +
//subtract 18 nucleotides, nucgap inter-ZF nucleotides, +1 for index correction for location of binding site
 +
table = table + "<td>" + (array1.lastIndex - 18 - nucgap) + "</td>";
 +
seqbottom = reverseComplement(array2[i].substring(0,9));
 +
table = table + "<td>" + seqbottom + "</td>";
 +
table = table + "<td>" + array2[i].substring(array2[i].length - 9,array2[i].length) + "</td>";
 +
table = table + "<td>" + array2[i] + "</td>";
 +
table = table + "</tr>";
 +
}
 +
 +
table = table + "</table><br /><br />"
 +
 +
document.getElementById("results").innerHTML = table;
 +
}
 +
*/
});
});
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     <option value="\w\w\w">NNN</option>
     <option value="\w\w\w">NNN</option>
</select><br />
</select><br />
-
<input type="text" id="bottom" value="Input NTPs here" class="graytext" />
+
<input type="text" id="bottominput" value="Input NTPs here" class="graytext" />
</td>
</td>
<td width="40%">
<td width="40%">
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     <option value="\w\w\w">NNN</option>
     <option value="\w\w\w">NNN</option>
</select><br />
</select><br />
-
<input type="text" id="topsearch" value="Input NTPs here" class="graytext" />
+
<input type="text" id="topinput" value="Input NTPs here" class="graytext" />
</td>
</td>
<td width="20%">
<td width="20%">
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<tr><td colspan="3">
<tr><td colspan="3">
<input type="button" value="Test (drop down menu)" onClick="findSites();" />
<input type="button" value="Test (drop down menu)" onClick="findSites();" />
-
<input type="button" id="findcustom" value="Test custom input" />
+
<input type="button" id="findcustom" value="Test custom input" onClick="findCustom();" />
<input type="button" value="Show me ALL binding sites!" onClick="findAllSites();" id="allsites"/>
<input type="button" value="Show me ALL binding sites!" onClick="findAllSites();" id="allsites"/>
</td></tr>
</td></tr>

Revision as of 03:47, 9 July 2011

<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> iGEM 2011 Zinc Finger Binding Site Finder

iGEM 2011 Zinc Finger Binding Site Finder

Justin Chew

Bottom Zinc Finger Array:

 Top Zinc Finger Array:

 Nucleotide Gap:

 

Retrieved from "http://2011.igem.org/Team:Harvard/ZF_Binding_Site_Finder"