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oligocalculator_sf2.html
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<Head>
<Title>Oligo Calculator (corrected by SF)</Title>
<SCRIPT LANGUAGE="JavaScript">
function Calculate(form) {
newOligo = new Oligo(form.oligoBox.value)
form.oligoBox.value = newOligo.Sequence
form.tmBox.value = newOligo.Tm()
form.gcBox.value = newOligo.GC()
form.mwBox.value = newOligo.MW()
form.odBox.value = newOligo.OD()
form.od2Box.value = newOligo.OD2()
form.lBox.value = newOligo.Sequence.length
}
function Oligo(theString)
{
this.Sequence = RemoveNonBase(theString)
this.aCount = CountChar(theString,"A")
this.cCount = CountChar(theString,"C")
this.gCount = CountChar(theString,"G")
this.tCount = CountChar(theString,"T")
this.Tm = Tm
this.GC = GC
this.MW = MW
this.OD = OD
this.OD2 = OD2
}
function OD()
{
if (this.Sequence.length > 0) {
return Math.round(1000000/(this.gCount * 11.7 + this.cCount * 7.3 + this.aCount * 15.4 + this.tCount * 8.8))
}
else
{
return ""
}
}
function OD2()
{
if (this.Sequence.length > 0) {
return (Math.round(1000000/(this.gCount * 11.7 + this.cCount * 7.3 + this.aCount * 15.4 + this.tCount * 8.8))/1000)
}
else
{
return ""
}
}
function MW()
{
if (this.Sequence.length > 0) {
return Math.round(313.2 * this.aCount + 328.2 * this.gCount + 289.2 * this.cCount + 304.2 * this.tCount - 60.96)
}
else
{
return ""
}
}
function GC()
{
if (this.Sequence.length > 0) {
return Math.round( 100 * ( this.gCount + this.cCount ) / this.Sequence.length )
}
else
{
return ""
}
}
function Tm()
{
if (this.Sequence.length > 0) {
if (this.Sequence.length < 14) {
return Math.round(2 * (this.aCount + this.tCount) + 4 * (this.gCount + this.cCount))
}
else {
return Math.round(64.9 + 41 * ((this.gCount + this.cCount - 16.4) / this.Sequence.length))
}
}
else {
return ""
}
}
function RemoveNonBase(theString) {
var returnString = ""
theString = theString.toUpperCase()
for ( var i = 0; i < theString.length; i++) {
if ((theString.charAt(i) == "A") || (theString.charAt(i) == "G") || (theString.charAt(i) == "C") || (theString.charAt(i) == "T")) {
returnString += theString.charAt(i)
}
}
return returnString
}
function CountChar(theString,theChar) {
var returnValue = 0
theString = theString.toUpperCase()
for ( var i = 0; i < theString.length; i++) {
if (theString.charAt(i) == theChar) {
returnValue ++
}
}
return returnValue
}
function Disallow(form) {
form.oligoBox.focus()
}
</SCRIPT>
</Head>
<Body>
<Center>
<H1>Oligo Calculator</H1>
<Form action="GET">
<table border ="6" align = center>
<tr align="center">
<td colspan=2 align=center>Enter Oligo Sequence in Box</td>
</tr>
<tr align="center">
<td colspan=2 align=center>
<TEXTAREA name="oligoBox" rows="2" cols="80" wrap=vitual align=left onChange="Calculate(this.form)"></TEXTAREA>
</td>
</tr>
<tr><td>
Length <Input name="lBox" size="5" onFocus="Disallow(this.form)">
</td>
<td>
Melting Temperature (T<sub>m</sub>) <Input name="tmBox" size="4" onFocus="Disallow(this.form)"> °C
</td></tr>
<tr><td>
<input name="gcBox" size="3" onFocus="Disallow(this.form)">% GC content
</td><td>
Molecular Weight: <input name="mwBox" size="9" onFocus="Disallow(this.form)"> daltons (g/mol)
</td></tr>
<tr><td>
<center><input type="button" value="Calculate" name="Calbutton" onClick="Calculate(this.form)"></center></td>
<td>
OD of 1 is equal to <input name="odBox" size="9" onFocus="Disallow(this.form)"> <B><FONT COLOR=#ff0000>nano</FONT>Molar (nM = pmol/ml).</B><br>
OD of 1 is equal to <input name="od2Box" size="9" onFocus="Disallow(this.form)"> <B><FONT COLOR=#ff0000>micro</FONT>Molar (µM = pmol/µl).
</td>
</tr>
</table>
</Form>
To use this calculator, you must be using Netscape 2.0 or later.<br>
This page was written in Javascript by <A HREF="mailto:buehler+@pitt.edu">Eugen Buehler</A><br>
Research Support Facilities<br>
Department of Molecular Genetics and Biochemistry<br>
University of Pittsburgh School of Medicine<br>
<hr width="95%" align=center>
Corrected and modified by <A HREF="mailto:stephanf@uio-pop.uio.no">Stephan Frye</A> (Jan. 2000)<br>
<hr width="95%" align=center>
<A HREF ="http://www.embl-heidelberg.de/~toldo/index.html"> Back to MGB Research Support Facilities Home Page</A>
</Center>
</Body>