Team:DTU Denmark/USERprogramoutputformat

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<a href="http://igem.grafiki.org/" CLASS=leftbar target="blank">Design your primers here</a><br><br>
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<b>Design your primers with PHUSER <a href="http://igem.grafiki.org/" CLASS=leftbar target="blank">here</a></b><br><br>
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Revision as of 21:14, 20 October 2009

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The project

Home The Team The Project Parts submitted Modelling Notebook

The redoxilator

 - Genetic design
- Applications and perspectives
- Results
- Safety considerations
The USER assembly standard

 - USER fusion of biobricks
USER fusion primer design software

 - Abstract
- Instructions
- Output format
The project


 The USER fusion primer design software: PHUSER
(Primer Help for USER)

PHUSER output format

Like the input options, the output from PHUSER is kept simple. First an overview of all needed primers is shown. The output is fairly self-explanatory, although it should be noted that primer consist of a fusion tail (ft) and a binding region (br), easily distinguished from one another by the occurence of the essential uracil. For example:


|--ft--| |-------br-------|
GGGTTAAU CAAATTATAGCCATACAG

IMPORTANT: Note that the entire sequence constitutes the primer. The space is simply added for illustrative purposes, and should be omitted when synthesizing the primers

Just below is the grafic overview of biobricks and primers. The first block illustrates the forward primer for biobrick 1, i.e. binding region to biobrick 1, and fusion tail to the selected USER cassette. The following blocks (the number depends on how many biobricks were entered), illustrate the region at which biobrick 1 is fused to biobrick 2 and so forth. The last 40 bases of biobrick 1 and the first 40 bases of biobrick 2 are displayed, along with the positioning of the fusion tails and binding regions for both reverse and forward primers. The last block of the graphic overview illustrated the last biobrick and its binding region to the selected cassette, diplayed in a similar fashion as described for the first block.

Lastly, the primers are displayed again, only this time with more detailed information, such as TM and GC ratio. More parameters are to be added to the output.

Design your primers with PHUSER here

Synthetic Biology

“Synthetic Biology is an art of engineering new biological systems that don’t exist in nature.”

-Paras Chopra & Akhil Kamma

In nature, biological molecules work together in complex systems to serve purposes of the cell. In synthetic biology these molecules are used as individual functional units that are combined to form tailored systems exhibiting complex dynamical behaviour. From ‘design specifications’ generated from computational modelling, engineering-based approaches enables the construction of such new specified gene-regulatory networks. The ultimate goal of synthetic biology is to construct systems that gain new functions, and the perspectives of the technology are enormous. It has already been used in several medical projects2 and is predicted to play a major role in biotech-production and environmental aspects.
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