<p style="font-family: quicksand;font-size:150%;">Screening by our software</p>
<p style="font-family: quicksand;font-size:150%;">Screening by our software</p>
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To minimize the manpower on screening of the switches, we constructed an online toehold switch design program. Apart from basic thermodynamic parameters, it also screens for other factors(please visit our <a href="https://2017.igem.org/Team:Hong_Kong-CUHK/Software"> software page </a>. Ultimately, the program generated a list of possible toehold switch sequences according to many different free energy parameters using the ViennaRNA library[2]. The graph below shows 394 possible H5 toehold switches generated by our software. The assumptions motioned earlier stated 3 very important parameters for the selection of switch candidates with the greatest possible performances: Switch MFE, ΔG<sub>RBS-linker</sub>, and ΔMFE. We applied these parameters to our switch selection process: We first chose the switches that with the highest ΔG<sub>RBS-linker</sub> (-3.8 kcal/mol). Among those switches, we chose the 3 switches with the lowest switch MFE and the highest ΔMFE.
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To minimize the manpower on screening of the switches, we constructed an online toehold switch design program. Apart from basic thermodynamic parameters, it also screens for other factors(please visit our <a href="https://2017.igem.org/Team:Hong_Kong-CUHK/Software"> software page </a>. Ultimately, the program generated a list of possible toehold switch sequences according to many different free energy parameters using the <a href="http://rna.tbi.univie.ac.at/cgi-bin/RNAWebSuite/barriers.cgi">ViennaRNA package</a>[2]. The graph below shows 394 possible H5 toehold switches generated by our software. The assumptions motioned earlier stated 3 very important parameters for the selection of switch candidates with the greatest possible performances: Switch MFE, ΔG<sub>RBS-linker</sub>, and ΔMFE. We applied these parameters to our switch selection process: We first chose the switches that with the highest ΔG<sub>RBS-linker</sub> (-3.8 kcal/mol). Among those switches, we chose the 3 switches with the lowest switch MFE and the highest ΔMFE.
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<p>Figure 2: ΔG<sub>RBS-linker</sub> of switch candidates generated from an example RNA sequence input by our software</p>
<p>Figure 2: ΔG<sub>RBS-linker</sub> of switch candidates generated from an example RNA sequence input by our software</p>