Archived Protocol

<!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"> <head> <meta http-equiv="Content-Type" content="text/html; charset=us-ascii" />  <title>PolyPro:Polynucleotide probe design. In situ hybridization parameters. Genes/mRNA based on polynucleotide probes. Specificity of polynucleotide probes.</title>  <meta name="description" content="In situ hybridization of genes/mRNA is based on polynucleotide probes. The specificity of polynucleotide probes has not been thoroughly investigated. A rational probe design concept was still missing, because the concept for oligonucleotide probe design cannot be transferred to polynucleotides" /> <meta name="Keywords" content="in situ, hybridization, genes, mRNA, polynucleotide, specificity, polynucleotide, probes, investigated, parameters" /> <meta name="ROBOTS" content="ALL" /> <meta http-equiv="Page-Enter" content="blendTrans(Duration=0.2)" /> <meta http-equiv="Page-Exit" content="blendTrans(Duration=0.2)" /> <link href="../style.css" rel="stylesheet" type="text/css" /> <link rel="shortcut icon" href="../favicon.ico" />  <script defer="defer" type="text/javascript" src="../scripts/menu_swap.js"></script> <script src="../scripts/AC_RunActiveContent.js" type="text/javascript"></script>  <script type="text/javascript"> var _gaq = _gaq || []; _gaq.push(['_setAccount', 'UA-3648054-1']); _gaq.push(['_trackPageview']); (function() { var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true; ga.src = ('https:' == document.location.protocol ? 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In situ hybridization parameters" width="1" height="1" /></td>  <td height="92" valign="top"> <center> <span class="Title16">PolyPro<br /> </span><span class="Title12">Polynucleotide probe design</span> </center> </td>  <td width="1" rowspan="4" bgcolor="#979797"><img src="../images/spacer.gif" alt="Genes/mRNA based on polynucleotide probes. Specificity of polynucleotide probes" width="1" height="1" /></td> </tr> <tr> <td height="336" valign="top"> <p align="justify"> In situ hybridization of genes and mRNA is most often based on polynucleotide probes. However, the specificity of polynucleotide probes has not been thoroughly investigated and a rational probe design concept was still missing, because the well established concept for oligonucleotide probe design cannot be transferred to polynucleotides. </p> <p align="justify"><br /> We recently developed a concept and software (PolyPro) for rational design of polynucleotide probe mixes to identify particular genes in defined taxa. PolyPro consists of three modules: a GenBank Taxonomy Extractor (GTE), a Polynucleotide Probe Designer (PPD) and a Hybridization Parameters Calculator (HPC). </p> <p align="justify"> </p> <p align="justify"> </p> <p align="justify"><span class="Title14">Download</span><br /> </p> <p align="justify"> </p> <p align="justify">The PolyPro is a freeware which runs on Windows platforms. </p> <p align="justify"> </p> <p align= "center"><a href="PolyPro.zip" class="center"><img src="../images/download free anim.gif" alt="Polynucleotide probe design" width="210" height="29" border="0" class="center" /></a></p> <p align="center">v1.8.4</p> <p class="Title14"> </p> <p class="Title14">Installion instructions </p> <ol> <li> Download the ZIP file</li> <li>Extract all files and folders from it (this is mandatory!)</li> <li>Run PolyPro.exe</li> </ol> <p> </p> <p class="Title14">Article</p> <p> </p> <p><a href="http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2010.02281.x/full" target="_blank">Article</a>: <a href="http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2010.02281.x/full" title="Polynucleotide probe design">GeneFISH – an in situ technique for linking gene presence and cell identity in environmental microorganisms</a><a href="#"></a></p> <p align="center"><img src="env logo.gif" alt="GeneFISH - an in situ technique for linking gene presence and cell identity in environmental microorganisms" width="453" height="58" border="0" /></p> <p> </p> <p> </p> <p class="Title14">Screen shots</p> <p> </p> <p> </p> <p align="center"><img src="screenshot.png" alt="PolyPro-rational design of polynucleotide probe mixes to identify particular genes in defined taxa" width="681" height="694" /></p> <p align="center"> </p> <p align="center"><img src="screenshot GTE.png" width="717" height="407" alt="GenBank Taxonomy Extractor (GTE)" /></p> <img src="../images/spacer.gif" width="1" height="1" /> <p> </p> <p align="center"><img src="screenshot HPC.png" width="873" height="728" alt="Polynucleotide Probe Designer (PPD)" /></p> <p align="center"> </p> <p align="center"><img src="screenshot PPD.png" width="751" height="962" alt="Hybridization Parameters Calculator (HPC)" /></p> <p align="center"> </p> <p align="center"> </p> <p align="center"> </p> <p align="center"> </p> <p align="center"> </p> <p align="center"><a href="PolyPro.zip" class="center"></a></p></td> </tr> <tr> <td height="29" valign="top"> </td> </tr> <tr> <td height="3" valign="top"><img src="../images/site_elements/3pixels_BottomLine.png" alt="In situ hybridization of genes/mRNA" width="948" height="3" /></td> </tr> </table> <table width="950" border="0" align="center" cellpadding="0" cellspacing="0" >  <tr> <td width="269" height="38" align="left" valign="middle"><span class="DevilsContract"><IMG width="1" height="1" SRC="http://acme-websign.info/counter.php?id=A3227419BD9205658CE12C330A2C36FA&style=6" alt="DNA sequence assembly and sequence analysis tool" border="0" /></span><span class="DevilsContract">  Copyright © Heracle BioSoft SRL</span></td> <td width="290" align="right" valign="middle" > </td> <td width="391" align="center" valign="middle" background="../images/site_elements/bott_yellow.png" class="menu02" > <p><a href="../contact/local_search.html"> Search</a>             <a href="../help/index.html">Support</a>            <a href="../contact/index.html">Contact</a> </p></td> </tr> </table> <p> </p> <p> </p> <p> </p> <p> </p> <p> </p> <style type="text/css">.ct {font:6pt;text-align:center;margin:0px}.ct img{border:0} .ct a,.ct a:visited{color:silver;text-decoration:none}.ct a:hover{color:gray;text-decoration:underline}</style><div class=ct><a href="http://acme-web-design.info"><img src="http://acme-web-design.info/counter.php?id=37495D4227E045C1894AA629E0DD41D2&style=28" alt="acme-web-design.info" /></a><br /><a href="http://acme-web-design.info">acme-web-design.info</a></div> </body> </html>