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<a href="https://yiplab.cse.cuhk.edu.hk/toehold/design.php"> | <a href="https://yiplab.cse.cuhk.edu.hk/toehold/design.php"> | ||
<center><img src="https://static.igem.org/mediawiki/2017/9/99/CUHK_software.jpg" width="100%" height="auto"></center> | <center><img src="https://static.igem.org/mediawiki/2017/9/99/CUHK_software.jpg" width="100%" height="auto"></center> | ||
</a> | </a> | ||
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+ | <center><h3>Overview of Software</h3></center> | ||
+ | <img src="https://static.igem.org/mediawiki/2017/3/38/CUHK_specification.jpg" width="20%" height="auto" style= "float: right"> | ||
+ | To reduce manpower, we wrote a program to automatically generate toehold switch sequences from target RNA input. We developed it to a website for the convenience of other iGEMers who are interested in toehold switch application. Although this website can execute many functions to reduce repetitive works for user, careful examination of thermodynamic parameters and RNA secondary structures is still encouraged to get a promising switch sequence. To help iGEMers get started, we would like to do a brief introduction on our website here. | ||
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+ | Our web tool takes as input the trigger RNA sequence and various design parameters, such as the promoter and RBS sequences to be inserted into the toehold switch, length of the recognition part of the trigger RNA and experiment temperature. Users can also choose to produce some optional outputs, such as rare codon count, minimum free energy and numbers of paired and unpaired bases, which could be useful for ranking the resulting list of candidate toehold switches. | ||
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+ | Upon receiving the inputs, our web tool carries out a number of steps to design the toehold switches (rightfigure). It first checks the format and validity of the inputs. After that, it uses a sliding window to consider every x consecutive bases of the trigger sequence as the potential recognition part, where x is the length of this part specified by the user. A toehold switch is constructed based on the subsequence in this window and the other input parameters. The toehold switch sequence is then subject to a sequence of tests, including the free of stop codons between the start codon and the downstream gene, and the lack of consecutive bases of the same type. If the switch can pass all these tests, free energy calculations will be performed next for the switch and trigger monomers and their interacting duplex, if the user chooses to output such information. Finally, optionally the sub-sequence in the window can be used to search the sequence database to check for highly similar off-target sequences. | ||
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<h1> Instructions </h1> | <h1> Instructions </h1> |
Revision as of 11:42, 29 October 2017