Team:Heidelberg/Modeling/miBSdesigner

From 2010.igem.org

(Difference between revisions)
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<title>BS designer for miRNA</title>
<title>BS designer for miRNA</title>
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
-
 
<style type="text/css">
<style type="text/css">
-
div.wrapper {width: 320px; padding:15px; border-width:3px; margin:auto; border-style:solid; border-color:#11526f; height: 340px; text-align:center;}
+
div.wrapper {width: 270px; padding:15px; border-width:3px; margin:auto; border-style:solid; border-color:#11526f; height: 220px; text-align:center;}
-
div.wrapper2 {width: 550px; padding:25px; border-width:3px; margin:auto; border-style:solid; border-color:#11526f; height: 550px; text-align:left; }
+
div.wrapper2 {width: 550px; padding:25px; border-width:3px; margin:auto; border-style:solid; border-color:#11526f; height: 670px; text-align:left; }
div.title {text-indent:30px;}
div.title {text-indent:30px;}
div.option {text-indent:50px; white-space:pre-wrap;}
div.option {text-indent:50px; white-space:pre-wrap;}
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div.suboption {text-indent:80px;}
div.suboption {text-indent:80px;}
div.clear {clear: both;}
div.clear {clear: both;}
-
div.reswrap2 { margin:auto; text-align:left; display:none; font-size:12pt;}
+
div.reswrap2 {margin:auto; text-align:left; display:none; font-size:12pt;}
-
.variaresult {font-size: 14pt; color: #11526f; font-weight: bold;}
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.variaresult {font-size: 12pt; color: #11526f; font-weight: bold;}
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</style>
</style>
-
 
</head>
</head>
     <body>
     <body>
     <form name="seqIn" action="">
     <form name="seqIn" action="">
-
    <div class="wrapper">
 
-
<img style="border-width: 0px;" src="http://2010.igem.org/wiki/images/c/c0/MiBSdesigner.png" width="300" height="182" />
 
-
<br><br>
 
-
<span style="font-family: Arial; color: #11526f; font-size: 18.0px; ">
 
-
Construction of microRNA binding sites </span>
 
-
<br>
 
-
</div>
 
-
<br>
 
<div class="wrapper2">
<div class="wrapper2">
-
                <center><span style="font-size: 17.0px;">
+
<center>
-
Sequence name </span>
+
<span style="font-size: 17.0px;">Sequence name </span>
<br>
<br>
<input type="text" name="name" id="name" size="40" value="hsa-miR122"/><br>
<input type="text" name="name" id="name" size="40" value="hsa-miR122"/><br>
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Spacer (inert sequence) </span><br>
Spacer (inert sequence) </span><br>
<input type="text" name="spacer" id="spacer" size="40" value="TTATATTTTATGACA"/></center>
<input type="text" name="spacer" id="spacer" size="40" value="TTATATTTTATGACA"/></center>
-
<br><br>
+
<br><br>
<input name="quality" value="perfect" onchange="chMd()" checked="checked" type="radio">
<input name="quality" value="perfect" onchange="chMd()" checked="checked" type="radio">
-
<span style="font-size: 18.0px;">
+
<span style="font-size: 17.0px;">
Perfect Binding Site </span>
Perfect Binding Site </span>
<br>
<br>
<input name="quality" value="bulge" onchange="chMd()" type="radio">
<input name="quality" value="bulge" onchange="chMd()" type="radio">
-
<span style="font-size: 18.0px;">
+
<span style="font-size: 17.0px;">
Imperfect Binding Site with 4 nt bulge (9-12) </span>
Imperfect Binding Site with 4 nt bulge (9-12) </span>
<br>
<br>
<input name="quality" value="personal" onchange="chMd()" type="radio">
<input name="quality" value="personal" onchange="chMd()" type="radio">
-
<span style="font-size: 18.0px;">
+
<span style="font-size: 17.0px;">
Personalized Binding Site </span>
Personalized Binding Site </span>
<br>
<br>
<br>
<br>
<div class="title">
<div class="title">
-
<span style="font-size: 18.0px; text-decoration: underline;">
+
<span style="font-size: 17.0px; text-decoration: underline;">
Seed sequence (1-8) </span></div>
Seed sequence (1-8) </span></div>
-
<div class="option">
+
<div class="option"><SELECT name="seed" onchange="chMd1()" disabled="disabled">
-
<SELECT name="seed" onchange="chMd1()" disabled="disabled">
+
<OPTION value="6mer">6mer                (2-7 paired)
<OPTION value="6mer">6mer                (2-7 paired)
<OPTION value="7merA1">7merA1          (1-7 paired)
<OPTION value="7merA1">7merA1          (1-7 paired)
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</SELECT></div>
</SELECT></div>
<div class="suboption">
<div class="suboption">
-
Customized <span style="color: #11526f; font-weight: bold; ">MISMATCH </span>position</div>
+
<span style="font-size: 15.0px;"> Customized </span>
 +
<span style="color: #11526f; font-size: 15.0px; font-weight: bold; ">MISMATCH </span>
 +
<span style="font-size: 15.0px;">position</span></div>
<div class="suboption">
<div class="suboption">
<input type="text" id="mis" size="30" disabled="disabled" value="2"/>
<input type="text" id="mis" size="30" disabled="disabled" value="2"/>
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<br>
<br>
<div class="title">
<div class="title">
-
<span style="font-size: 18.0px; text-decoration: underline;">
+
<span style="font-size: 17.0px; text-decoration: underline;">
-
Supplementary region </span>
+
Supplementary region </span></div>
-
</div>
+
<div class="option"><SELECT name="comp" onchange="chMd2()" disabled="disabled">
-
<div class="option">
+
-
<SELECT name="comp" onchange="chMd2()" disabled="disabled">
+
<OPTION value="3">3                  (14-16 paired)
<OPTION value="3">3                  (14-16 paired)
<OPTION value="4">4                  (13-16 paired)
<OPTION value="4">4                  (13-16 paired)
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</SELECT></div>
</SELECT></div>
<div class="suboption">
<div class="suboption">
-
Customized <span style="color: #11526f; font-weight: bold; ">MATCH </span>positions (input numbers from 9 to 22)</div>
+
<span style="font-size: 15.0px;"> Customized </span>
 +
<span style="color: #11526f; font-size: 15.0px; font-weight: bold; ">MATCH </span>
 +
<span style="font-size: 15.0px;">positions (input numbers from 9 to 22)</span></div>
<div class="suboption">
<div class="suboption">
<input type="text" id="match" size="30" disabled="disabled" value="10, 15, 16, 17, 18, 19, 20"/></div>
<input type="text" id="match" size="30" disabled="disabled" value="10, 15, 16, 17, 18, 19, 20"/></div>
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<br>
<br>
<div class="title">
<div class="title">
-
<span style="font-size: 14pt; text-decoration: underline;">
+
<span style="font-size: 17.0px; text-decoration: underline;">
Modify AU content </span>
Modify AU content </span>
</div>
</div>
-
<div class="optionl"><input name="AU" value="-1" type="checkbox">A in position -1</div>
+
<div class="optionl"><input name="AU" value="-1" type="checkbox"><span style="font-size: 15.0px;">A in position -1</span></div>
-
<div class="optionr"><input name="AU" value="0" type="checkbox">A in position 0                   </div>
+
<div class="optionr"><input name="AU" value="0" type="checkbox"><span style="font-size: 15.0px;">A in position 0 </span></div>
<div class="clear">
<div class="clear">
-
<div class="optionl"><input name="AU" value="1" disabled="disabled" type="checkbox">A in position 1</div>
+
<div class="optionl"><input name="AU" value="1" disabled="disabled" type="checkbox"><span style="font-size: 15.0px;">A in position 1</span></div>
-
<div class="optionr"><input name="AU" value="8" disabled="disabled" type="checkbox">A in position 8                   </div></div>
+
<div class="optionr"><input name="AU" value="8" disabled="disabled" type="checkbox"><span style="font-size: 15.0px;">A in position 8 </span></div></div>
<div class="clear">
<div class="clear">
-
<div class="optionl"><input name="AU" value="9" disabled="disabled" type="checkbox">A in position 9</div>
+
<div class="optionl"><input name="AU" value="9" disabled="disabled" type="checkbox"><span style="font-size: 15.0px;">A in position 9</span></div>
-
<div class="optionr"><input name="AU" value="10" disabled="disabled" type="checkbox">A in position 10                 </div></div> <br>
+
<div class="optionr"><input name="AU" value="10" disabled="disabled" type="checkbox"><span style="font-size: 15.0px;">A in position 10</span></div></div><br>
<div class="clear">
<div class="clear">
<br>
<br>
-
<div class="option"><span style="font-size: 18px; text-decoration: underline;">Sticky ends for integration in plasmid: </span></div>
+
<div class="title"><span style="font-size: 17.0px; text-decoration: underline;">Sticky ends for integration in plasmid: </span></div>
-
<div class="option">  <SELECT id="stickyends" name="stickyends" onchange="chMd3()">
+
<div class="option">  <SELECT name="stickyends" onchange="chMd3()">
<OPTION SELECTED value="none">None
<OPTION SELECTED value="none">None
<OPTION value="BBB">Biobricks Standard RFC-12
<OPTION value="BBB">Biobricks Standard RFC-12
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<OPTION value="custom">Custom sequence
<OPTION value="custom">Custom sequence
</SELECT></div>
</SELECT></div>
-
<div class="option">      Customized:    5'<input type="text" id="end5" size="15" disabled="disabled"/>        3'<input type="text" id="end3" size="15" disabled="disabled"/>
+
<div class="option"><span style="font-size: 15.0px;">      Customized:    5'</span><input type="text" id="end5" size="15" disabled="disabled"/>        <span style="font-size: 15.0px;">3'</span><input type="text" id="end3" size="15" disabled="disabled"/>
</div>
</div>
<center>
<center>
-
<input value="      Get your Binding Site!      " type="button" onclick="SBS(seqIn)">
+
<input value="      Get your Binding Site!      " type="button" onClick="SBS(seqIn)">
</center>
</center>
<br>
<br>
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</form>
</form>
</div>
</div>
-
<br>
+
<br>
 +
<div class="reswrap2" id="resultdiv">
 +
<div class="variaresult">Name of primer 1</div>
 +
<textarea name="NamA" id="NamA" wrap=SOFT></textarea><br>
 +
<div class="variaresult">Sequence of primer 1</div>
 +
<textarea name="seqA" id="seqA" wrap=SOFT></textarea><br>
 +
<div class="variaresult">Name of primer 2</div>
 +
<textarea name="NamB" id="NamB" wrap=SOFT></textarea><br>
 +
<div class="variaresult">Sequence of primer 2</div>
 +
<textarea name="seqB" id="seqB" wrap=SOFT></textarea><br>
 +
</div>
</body>
</body>
-
<script type="text/javascript" src="http://2010.igem.org/wiki/images/2/24/Final_code_miBS_HD2010.txt"></script>
+
<script type="text/javascript" src="final_code_miBS_HD2010.txt"> </script>
</html>
</html>
{{:Team:Heidelberg/Pagemiddle}}
{{:Team:Heidelberg/Pagemiddle}}
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<div class="reswrap2" id="resultdiv">
<div class="reswrap2" id="resultdiv">
<html>
<html>
-
                 <br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br>
+
                 <div class="wrapper">
 +
<img style="border-width: 0px;" src="http://2010.igem.org/wiki/images/c/c0/MiBSdesigner.png" width="280" height="158" />
 +
<br><br>
 +
<span style="font-family: Arial; color: #11526f; font-size: 18.0px; font-weight: bold;">
 +
Construction of microRNA binding sites </span>
 +
<br>
 +
</div>
 +
<br><br><br><br><br><br><br><br><br><br><br><br><br><br><br>
<div class="variaresult">Name of primer 1</div>
<div class="variaresult">Name of primer 1</div>
<textarea name="NamA" cols=30 rows=1 id="NamA" wrap=SOFT></textarea><br><br>
<textarea name="NamA" cols=30 rows=1 id="NamA" wrap=SOFT></textarea><br><br>

Revision as of 14:37, 25 October 2010

BS designer for miRNA
Sequence name

microRNA Sequence ( 5' -> 3')

Spacer (inert sequence)


Perfect Binding Site
Imperfect Binding Site with 4 nt bulge (9-12)
Personalized Binding Site

Seed sequence (1-8)
Customized MISMATCH position

Supplementary region
Customized MATCH positions (input numbers from 9 to 22)


Modify AU content
A in position -1
A in position 0
A in position 1
A in position 8
A in position 9
A in position 10


Sticky ends for integration in plasmid:
Customized: 5' 3'


Name of primer 1

Sequence of primer 1

Name of primer 2

Sequence of primer 2



Construction of microRNA binding sites















Name of primer 1


Sequence of primer 1


Name of primer 2


Sequence of primer 2