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Team:DTU Denmark/USERprograminstructions
From 2009.igem.org
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| - | The redoxilator | + | The redoxilator<br> |
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<a href="https://2009.igem.org/Team:DTU_Denmark/genetic_design" CLASS=leftbar>- Genetic design</a><br> | <a href="https://2009.igem.org/Team:DTU_Denmark/genetic_design" CLASS=leftbar>- Genetic design</a><br> | ||
<a href="https://2009.igem.org/Team:DTU_Denmark/applications" CLASS=leftbar>- Applications and perspectives</a><br> | <a href="https://2009.igem.org/Team:DTU_Denmark/applications" CLASS=leftbar>- Applications and perspectives</a><br> | ||
| - | + | <a href="https://2009.igem.org/Team:DTU_Denmark/safety" CLASS=leftbar>- Safety considerations</a><br> | |
| - | <a href="https://2009.igem.org/Team:DTU_Denmark/safety" CLASS=leftbar>- Safety considerations</a | + | |
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| - | <br>The USER assembly standard | + | <br>The USER assembly standard<br> |
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| - | <a href="https://2009.igem.org/Team:DTU_Denmark/USERprinciple" CLASS=leftbar>- USER fusion of biobricks</a | + | <a href="https://2009.igem.org/Team:DTU_Denmark/USERprinciple" CLASS=leftbar>- USER fusion of biobricks</a><br> |
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| - | <br>USER fusion primer design software | + | <br>USER fusion primer design software<br> |
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<a href="https://2009.igem.org/Team:DTU_Denmark/USERprogram" CLASS=leftbar>- Abstract</a><br> | <a href="https://2009.igem.org/Team:DTU_Denmark/USERprogram" CLASS=leftbar>- Abstract</a><br> | ||
<a href="https://2009.igem.org/Team:DTU_Denmark/USERprograminstructions" CLASS=leftbar>- Instructions</a><br> | <a href="https://2009.igem.org/Team:DTU_Denmark/USERprograminstructions" CLASS=leftbar>- Instructions</a><br> | ||
<a href="https://2009.igem.org/Team:DTU_Denmark/USERprogramoutputformat" CLASS=leftbar>- Output format</a><br> | <a href="https://2009.igem.org/Team:DTU_Denmark/USERprogramoutputformat" CLASS=leftbar>- Output format</a><br> | ||
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| + | <br>Experimental results<br> | ||
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| + | <a href="https://2009.igem.org/Team:DTU_Denmark/results" CLASS=leftbar>- Results and discussion</a><br> | ||
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| - | <b>The project</b | + | <b>The project</b><br><br> |
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<strong>Achievements</strong><br> | <strong>Achievements</strong><br> | ||
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Latest revision as of 03:16, 22 October 2009
| Home | The Team | The Project | Parts submitted | Modelling | Notebook |
|
- Applications and perspectives - Safety considerations
- Instructions - Output format
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The project The USER fusion primer design software: PHUSER (Primer Help for USER) PHUSER user manual We have put a lot of thought and consideration into which user-definable parameters to include. In the end, we decided that a user-friendly input was the best solution for the beta version of PHUSER. Further down the line, the program can be customized for high-end users, and advanced options made available upon request. For now we keep it simple, and ask only for three main inputs: 1. Name of biobrick (essentially you can call it whatever you wish), and; 2. Sequence of biobrick (pasted as single-stranded DNA from 5' to 3'). NOTE: Only A's, T's, G's, and C's are accepted as input, i.e. no FASTA-headers or spaces (line shifts are ok). 3. Your choice of USER cassette. For now only one is available, but more will follow shortly. As a default in the interface, only two biobrick-submission boxes are available to begin with. If you wish to fuse more than two biobricks in the same reaction, simply click "add another biobrick" and another submission box will appear. The maximum capacity is nine biobricks (may be subject to change). Design your primers with PHUSER here |
Achievements Redox sensing device Two novel genes have been designed and synthesized each comprised of 5 genetic elements. Together they function as a device termed the Redoxilator that can sense the internal redox state of a yeast cell, and output a reporter signal. Extensive mathematical modelling was performed to simulate how the construct would operate in vivo. Biobricks DNA of several new biobricks have been designed and submitted including a yeast optimized GFP reporter protein, a protein degradation sequence and a fast degradable yeast GFP. (Bronze medal) We have demonstrated that our USER fusion biobrick works as expected and documented it (silver medal) USER fusion Assembly standard A new biobrick assembly standard that allows the rapid construction of multi-part devices have been developed and documented. The assembly standard offers many benefits: All restriction sites are allowed, multiple biobricks can be joined in one step, the result is scar-free making it ideal for protein fusions and more. (Gold medal) USER-fusion primer design software A novel and very useful software tool have been developed that can automatically design the optimal primers for USER fusion assembly of 2-9 biobricks, taking several parameters into account. |
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