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Team:Dundee/Software
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<li><a href="/Team:Dundee/dnaapp" title="DNA App">DNA App</a></li> | <li><a href="/Team:Dundee/dnaapp" title="DNA App">DNA App</a></li> | ||
<li class="current_page_item" ><a href="/Team:Dundee/Software" title="Software">Software</a></li> | <li class="current_page_item" ><a href="/Team:Dundee/Software" title="Software">Software</a></li> | ||
| + | <li ><a href="/Team:Dundee/HumanPractices" title="Human Practices">Human Practices</a></li> | ||
</ul> | </ul> | ||
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<div class="largepost2"> | <div class="largepost2"> | ||
| - | <h2>The Gene Cutter</h2> | + | <h2>The Gene Cutter & The Gene Slicer</h2> |
| - | <p>The Gene Cutter | + | <p>The Gene Cutter (iPhone app) and The Gene Slicer (Android app) are gene cutting tools aimed to assist synthetic biologists. The apps have two functions to help restriction mapping of nucleotide sequences. The apps are able to search a sequence for a specific enzyme and can also return a list of enzymes not present in the sequence. |
The app is available for free in both the<a href = "http://itunes.apple.com/gb/app/the-gene-cutter/id457285857?mt=8"><b> iPhone App Store</b> </a>and the<a href= "http://market.android.com/details?id=me.davegibson.cutterapp"> <b>Android Market.</b></a></p> | The app is available for free in both the<a href = "http://itunes.apple.com/gb/app/the-gene-cutter/id457285857?mt=8"><b> iPhone App Store</b> </a>and the<a href= "http://market.android.com/details?id=me.davegibson.cutterapp"> <b>Android Market.</b></a></p> | ||
| + | <p>As of Friday October 28, 2011, both Android apps had over 950 downloads worldwide, while the iPhone apps had been downloaded over 400 times. | ||
</p> | </p> | ||
</div> | </div> | ||
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<div class="largepost2"> | <div class="largepost2"> | ||
| - | <h2>Gene | + | <h2>The Gene Synthesiser</h2> |
| - | <p> | + | <p>Many synthetic biology projects involve the heterologous expression of foreign genes in a host such as <i>E. coli</i> / <i>S. cerevisiae</i> etc. For successful and efficient translation, the codon usage of the newly introduced gene must be optimised to match the tRNA pool of the host organism. However, if one simply picked the most common codon for each amino acid, the rate of translation would likely be extremely fast across the entire gene. This may lead to subtle characteristics of translation being lost. For example, it has been suggested that in certain regions of the gene, the source organism may ‘choose’ a short run of rare codons, in order to slow down translation in that region. This slowing of the emerging polypeptide from the ribosome has been suggested to facilitate the correct folding of the heterologous protein and/or allow time for the insertion of essential co-factors. <b><a href = "https://2011.igem.org/Team:Dundee/References">[19]</a></b> These regions of "slow" translation, may occur in loops between different domains of the protein. It may be therefore important for certain genes to maintain this pattern of fast-to-slow translation in the target organism. |
| + | “Gene Synthesiser” is a java application that makes this possible by enabling codon usage pattern-matching. The application analyses the patterns of codon usage of the gene that one wants to express, in its native organism and generates new synthetic DNA sequence optimised for the codon usage of the new target organism, yet matching any patterns of rare to common codons. Gene Synthesiser utilises codon usage data for over 35000 organisms. <b><a href = "https://2011.igem.org/Team:Dundee/References">[20]</a></b>.</p> | ||
| + | |||
| + | <p>Instructions:</p> | ||
| + | <p>Enter the DNA sequence of the gene in its native organism and select the original organism from the dropdown box. Then select the new host you wish to express this gene in from the second drop down box. Gene Synthesiser will generate a new synthetic DNA sequence optimised for the codon usage of the new target organism, yet closely matching any patterns of rare to common codons from the original gene.</p> | ||
| + | |||
| + | <p>To try the Gene Synthesiser for yourself click <a href = "http://www.dave-gibson.net/projects/genesynthesis"><b>HERE</b> </a></p> | ||
</div> | </div> | ||
Latest revision as of 15:31, 28 October 2011
The University of Dundee
iGem 2011
The Lazy Scientist
The Lazy Scientist is a translation tool aimed to assist synthetic biologists. The app has a number of functions including DNA to amino acid translation, back translation, reverse, complement and reverse complement. The app also contains a genetic codon lookup table allowing all corresponding codons for an amino acid to be looked up. The app is available for free in both the iPhone App Store and the Android Market.
The Gene Cutter & The Gene Slicer
The Gene Cutter (iPhone app) and The Gene Slicer (Android app) are gene cutting tools aimed to assist synthetic biologists. The apps have two functions to help restriction mapping of nucleotide sequences. The apps are able to search a sequence for a specific enzyme and can also return a list of enzymes not present in the sequence. The app is available for free in both the iPhone App Store and the Android Market.
As of Friday October 28, 2011, both Android apps had over 950 downloads worldwide, while the iPhone apps had been downloaded over 400 times.
The Gene Synthesiser
Many synthetic biology projects involve the heterologous expression of foreign genes in a host such as E. coli / S. cerevisiae etc. For successful and efficient translation, the codon usage of the newly introduced gene must be optimised to match the tRNA pool of the host organism. However, if one simply picked the most common codon for each amino acid, the rate of translation would likely be extremely fast across the entire gene. This may lead to subtle characteristics of translation being lost. For example, it has been suggested that in certain regions of the gene, the source organism may ‘choose’ a short run of rare codons, in order to slow down translation in that region. This slowing of the emerging polypeptide from the ribosome has been suggested to facilitate the correct folding of the heterologous protein and/or allow time for the insertion of essential co-factors. [19] These regions of "slow" translation, may occur in loops between different domains of the protein. It may be therefore important for certain genes to maintain this pattern of fast-to-slow translation in the target organism. “Gene Synthesiser” is a java application that makes this possible by enabling codon usage pattern-matching. The application analyses the patterns of codon usage of the gene that one wants to express, in its native organism and generates new synthetic DNA sequence optimised for the codon usage of the new target organism, yet matching any patterns of rare to common codons. Gene Synthesiser utilises codon usage data for over 35000 organisms. [20].
Instructions:
Enter the DNA sequence of the gene in its native organism and select the original organism from the dropdown box. Then select the new host you wish to express this gene in from the second drop down box. Gene Synthesiser will generate a new synthetic DNA sequence optimised for the codon usage of the new target organism, yet closely matching any patterns of rare to common codons from the original gene.
To try the Gene Synthesiser for yourself click HERE
