Team:Harvard/ZF Binding Site Finder

From 2011.igem.org

(Difference between revisions)
Line 238: Line 238:
}
}
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});
 +
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// findAllSites function
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$("#findallsites").click(function () {
 +
 +
//initialize check variable, if check != 0 then results were found, else no results found
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var check = 0;
 +
 +
//get test sequence
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var testseq = $("#sequence").val().toUpperCase();
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//build array of nucleotides
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var nucleotides = new Array("G", "C", "T", "A");
 +
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//initialize table string to hold code for table
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var table = "";
 +
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//loop multidimensional array to iterate all possible zinc fingers, each array has 4 elements for 4 nucleotides
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var nest = new Array(4);
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for(var a=0; a<4; a++)
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{
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nest[a] = new Array(4);
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for(var b=0; b<4; b++)
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{
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nest[a][b] = new Array(4);
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for(var c=0; c<4; c++)
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{
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nest[a][b][c] = new Array(4);
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for(var d=0; d<4; d++)
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{
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nest[a][b][c][d] = new Array(4);
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for(var e=0; e<4; e++)
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{
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nest[a][b][c][d][e] = new Array(4);
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for(var f=0; f<4; f++)
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{
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//build regular expression for each nucleotide combination
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nest[a][b][c][d][e][f] = "\\w\\w" + reverseComplement(nucleotides[c]) + "\\w\\w" + reverseComplement(nucleotides[b]) + "\\w\\w" + reverseComplement(nucleotides[a]);
 +
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//add in x NTPs between first and second finger
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var nucgap = $("#gap").val();
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for(i=0;i<nucgap;i++){
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nest[a][b][c][d][e][f] = nest[a][b][c][d][e][f] + "\\w";
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}
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//finish constructing dynamic regular expression
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nest[a][b][c][d][e][f] = nest[a][b][c][d][e][f] + nucleotides[d] + "\\w\\w" + nucleotides[e] + "\\w\\w" + nucleotides[f] + "\\w\\w";
 +
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//find all instances of current nucleotide combination
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var array1 = new RegExp(nest[a][b][c][d][e][f], "gi");
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var array2 = testseq.match(array1);
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//do nothing if no result found
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if(testseq.search(array1) == -1)
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{
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} else {
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//add table heading for each combo
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table = table + "<tr><td colspan='4'><b>" + "Bottom finger: " + nucleotides[a] + nucleotides[b] + nucleotides[c] + " Top finger: " + nucleotides[d] + nucleotides[e] + nucleotides[f] + "</b></td></tr>";
 +
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var revComp = "";
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var seqtwo = "";
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var index = 0;
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for(i=0;i<array2.length;i++)
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{
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array1.test(testseq);
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table = table + "<tr>";
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//subtract 18 nucleotides, nucgap inter-ZF nucleotides, +1 for index correction for location of binding site
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table = table + "<td>" + (array1.lastIndex - 18 - nucgap) + "</td>";
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seqbottom = reverseComplement(array2[i].substring(0,9));
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table = table + "<td>" + seqbottom + "</td>";
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table = table + "<td>" + array2[i].substring(array2[i].length - 9,array2[i].length) + "</td>";
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table = table + "<td>" + array2[i] + "</td>";
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table = table + "</tr>";
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}
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check++;
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}
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}
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}
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}
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}
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}
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}
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//only build table if check is nonzero
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if(check == 0)
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{
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$("#results").html("No binding sites found, unfortunately :(");
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} else {
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//add table preamble
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var 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>" + table;
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//add table tail
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table = table + "</table><br /><br />"
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//write table to page
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$("#results").html(table);
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}
});
});
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<input type="button" id="findsites" value="Test (drop down menu)" />
<input type="button" id="findsites" value="Test (drop down menu)" />
<input type="button" id="findcustom" value="Test custom input" />
<input type="button" id="findcustom" value="Test custom input" />
-
<input type="button" value="Show me ALL binding sites!" onClick="findAllSites();" id="allsites"/>
+
<input type="button" id="findallsites" value="Show me ALL binding sites!" />
</td></tr>
</td></tr>
</table>
</table>

Revision as of 04:05, 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"