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Team:Harvard/ZF Binding Site Finder
From 2011.igem.org
(Difference between revisions)
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<html xmlns="http://www.w3.org/1999/xhtml"> | <html xmlns="http://www.w3.org/1999/xhtml"> | ||
<head> | <head> | ||
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return output; | return output; | ||
| + | } | ||
| + | |||
| + | // findSites function | ||
| + | $("#findsites").click(function() { | ||
| + | |||
| + | //get DNA sequence | ||
| + | var testseq = $("#sequence").val().toUpperCase(); | ||
| + | |||
| + | //get zinc finger arrays for searching | ||
| + | var zf11 = $("#11").val(); | ||
| + | var zf12 = $("#12").val(); | ||
| + | var zf13 = $("#13").val(); | ||
| + | var zf21 = $("#21").val(); | ||
| + | var zf22 = $("#22").val(); | ||
| + | var zf23 = $("#23").val(); | ||
| + | |||
| + | //start building regular expression from ZF fingers | ||
| + | var siteExp = "(" + zf23 + zf22 + zf21; | ||
| + | |||
| + | //add in x NTPs between first and second finger | ||
| + | var nucgap = $("#gap").value; | ||
| + | for(i=0;i<nucgap;i++){ | ||
| + | siteExp = siteExp + "\\w"; | ||
| + | } | ||
| + | |||
| + | //finish building regular expression | ||
| + | siteExp = siteExp + zf11 + zf12 + zf13 + "){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) | ||
| + | { | ||
| + | $("#results").html("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 />" | ||
| + | |||
| + | $("#results").html(table); | ||
| + | } | ||
} | } | ||
| Line 253: | Line 316: | ||
</tr> | </tr> | ||
<tr><td colspan="3"> | <tr><td colspan="3"> | ||
| - | <input type="button" 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" value="Show me ALL binding sites!" onClick="findAllSites();" id="allsites"/> | ||
Revision as of 03:58, 9 July 2011
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