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| − | <div class="column full_size judges-will-not-evaluate"> | + | <h1>Software</h1> |
| − | <h3>★ ALERT! </h3> | + | <h2>Peroxisome Primer Designer</h2> |
| − | <p> This page is used by the judges to evaluate your team for the <a href="https://2017. igem.org/Judging/Medals">medal criterion</a> or <a href=" https://2017.igem.org/Judging/Awards"> award listed above</a>. </p> | + | <p> We created a small software package to enable fast primer design for peroxisomal matrix import and matrix integration. The package uses <a href=" #"> primer3</a> to calculate the thermodynamic characteristics of the primer pair.</p> |
| − | <p> Delete this box in order to be evaluated for this medal criterion and/or award. See more information at <a href="https://2017.igem.org/Judging/Pages_for_Awards"> Instructions for Pages for awards</a>.</p> | + | <p> On the first screen you can paste the sequence of the protein you want to import or integrate into the peroxisome.< /p> |
| − | </div> | + | <img src="https://static.igem.org/mediawiki/2017/2/2d/T--Cologne-Duesseldorf--01-sequence.PNG"> |
| − | <div class="clear"></div> | + | < p> On the second screen you can choose the import or integration mechanism into the peroxisome. The C-terminal matrix import corresponds to < a href=" #"> PEX5</ a> import, the N-terminal to < a href=""> PEX7</ a>. The N-terminal import should only be used when the protein is sensitive to C-terminal modifications. The C-terminal integration corresponds to the <a href=" #"> Pex3/Pex19-dependent pathway</a>, the N-terminal integration to the <a href=" #"> ER-dependent pathway</a>. |
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| − | | + | Furthermore the favored melting temperature can be set. |
| − | <div class="column half_size"> | + | </p> |
| − | <h1>Software</h1>
| + | <img src="https://static.igem.org/mediawiki/2017/4/42/T--Cologne-Duesseldorf--02-options.PNG"> |
| − | <h3>Best Software Tool Special Prize</h3>
| + | <p>Finally the output screen shows the primer sequences, the respective melting and hairpin temperatures of the primers and the temperature for dimer formation. Note that the hairpin and dimer calculations are done without the added targeting sequences, as they can easily exceed the 60 bp limit for primer3.</p> |
| − | <p>Regardless of the topic, iGEM projects often create or adapt computational tools to move the project forward. Because they are born out of a direct practical need, these software tools (or new computational methods) can be surprisingly useful for other teams. Without necessarily being big or complex, they can make the crucial difference to a project's success. This award tries to find and honor such "nuggets" of computational work.
| + | <img src="https://static.igem.org/mediawiki/2017/1/16/T--Cologne-Duesseldorf--03-results.PNG"> |
| − | | + | <h2>Download</h2> |
| − | | + | < p> Sadly we could not compile the software into a standalone software, but you can download the python file <a href="https:// static.igem.org/ mediawiki/ 2017/ e/ec/Peroxisome_Primer_Designer.zip"> here</a> .</ p> |
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| − | To compete for the <a href=" https://2017.igem.org/Judging/Awards"> Best Software Tool prize</a>, please describe your work on this page and also fill out the description on the <a href=" https://2017.igem.org/Judging/Judging_Form"> judging form</a>. | + | </body> |
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| − | You must also delete the message box on the top of this page to be eligible for this prize.
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| − | <h5> Inspiration </h5>
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| − | <p>
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| − | Here are a few examples from previous teams:
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| − | </p>
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| − | <ul>
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| − | <li><a href="https://2016.igem.org/Team:BostonU_HW">2016 BostonU HW</a></li>
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| − | <li><a href="https://2016.igem.org/Team:Valencia_UPV">2016 Valencia UPV</a></li>
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| − | <li><a href="https://2014.igem.org/Team:Heidelberg/Software">2014 Heidelberg</a></li> | + | |
| − | < li><a href="https:// 2014.igem.org/ Team:Aachen/ Project/ Measurement_Device#Software"> 2014 Aachen</a></ li> | + | |
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Software
Peroxisome Primer Designer
We created a small software package to enable fast primer design for peroxisomal matrix import and matrix integration. The package uses primer3 to calculate the thermodynamic characteristics of the primer pair.
On the first screen you can paste the sequence of the protein you want to import or integrate into the peroxisome.
On the second screen you can choose the import or integration mechanism into the peroxisome. The C-terminal matrix import corresponds to PEX5 import, the N-terminal to PEX7. The N-terminal import should only be used when the protein is sensitive to C-terminal modifications. The C-terminal integration corresponds to the Pex3/Pex19-dependent pathway, the N-terminal integration to the ER-dependent pathway.
Furthermore the favored melting temperature can be set.
Finally the output screen shows the primer sequences, the respective melting and hairpin temperatures of the primers and the temperature for dimer formation. Note that the hairpin and dimer calculations are done without the added targeting sequences, as they can easily exceed the 60 bp limit for primer3.
Download
Sadly we could not compile the software into a standalone software, but you can download the python file here.
