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Team:DTU Denmark/USERprogramoutputformat
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<font face="Lucida Console" size="2.5"> | <font face="Lucida Console" size="2.5"> | ||
| - | |--ft--| | + | |--ft--| |-------br-------|<br> |
GGGTTAAU CAAATTATAGCCATACAG | GGGTTAAU CAAATTATAGCCATACAG | ||
</font><br><br> | </font><br><br> | ||
| - | <p align="justify"><b>Note that the entire sequence constitute the primer | + | <p align="justify"><b>IMPORTANT: Note that the entire sequence constitute the primer. The space is simply added for illustrative purposes, and should be omitted when synthesizing the primers<b/><br><br> |
| - | Just below is the grafic overview of biobricks and primers. The first block illustrates the forward primer for biobrick 1 | + | 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.<br><br> |
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| + | Lastly, the primers are displayed again, only this time with more detailed information, such as T<sub>M</sub> and GC ratio. More parameters are to be added to the output.<br><br> | ||
Revision as of 13:56, 18 October 2009
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The redoxilator - Introduction - Results - Applications and perspectives The USERTM assembly standard - Principle - Proof of concept - Manual USERTM fusion primer design software - Abstract - Instructions - Output format |
The project USER fusion primer design software Program output format Like the input options, the output from the program 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 constitute the primer. The space is simply added for illustrative purposes, and should be omitted when synthesizing the primers |
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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