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Team:SUSTC-Shenzhen-B/future plan
From 2012.igem.org
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| - | <h2>Future Version of Our Software</h2> | + | <h2><p>Future Version of Our Software</p></h2> |
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| - | <h3><b>Introduction</b></h3> | + | </font> |
| - | <p>Now our pc software and online tool can predict the efficiency of rho-independent terminator. The algorithm is based on two scoring systems, which were created by d'Aubenton Carafa and Elena A Lesnik respectively. The scoring systems were created to predict intrinsic terminators. So when we use them to predict terminator efficiency, the parameters of the score calculation may not be the best.What’s more, if the efficiency of their terminator is not suitable for users, they have to modify the terminator themselves. In the future, we want to solve these two problems.</p> | + | <h3><font face="Arial, Helvetica"><b><font color="#0000FF">Introduction</font></b></font></h3> |
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| + | <p>Now our pc software and online tool can predict the efficiency of rho-independent terminator. The algorithm is based on two scoring systems, which were created by d'Aubenton Carafa and Elena A Lesnik respectively. The scoring systems were created to predict intrinsic terminators. So when we use them to predict terminator efficiency, the parameters of the score calculation may not be the best.What’s more, if the efficiency of their terminator is not suitable for users, they have to modify the terminator themselves. In the future, we want to solve these two problems.</p> | ||
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| - | <h3><b>Future Plan</b></h3> | + | </font> |
| + | <h3><font face="Arial, Helvetica"><b><font color="#0000FF">Future Plan</font></b></font></h3> | ||
| + | <font face="Arial, Helvetica"> | ||
<p>1. Mutate the coefficients of the scoring formular to help get the best simulation formular of score and efficiency</p> | <p>1. Mutate the coefficients of the scoring formular to help get the best simulation formular of score and efficiency</p> | ||
<p>D Score = nT * 18.16 + deltaG / LH * 96.59 – 116.87</p> | <p>D Score = nT * 18.16 + deltaG / LH * 96.59 – 116.87</p> | ||
<p> (nT is the score of t tail, deltaG is the energy change of the stemloop formation and LH is the length of stemloop sequence.)</p> | <p> (nT is the score of t tail, deltaG is the energy change of the stemloop formation and LH is the length of stemloop sequence.)</p> | ||
<p> Here the coefficient of each terms can be adjusted to help make the best simulation between score and efficiency. Maybe we can treat efficiency as a function of those terms directly, which means we can calculate terminator efficiency using nt, deltaG and LH directly without calculating the score first, ie : Efficiency = E(nt, deltaG,LH).</p> | <p> Here the coefficient of each terms can be adjusted to help make the best simulation between score and efficiency. Maybe we can treat efficiency as a function of those terms directly, which means we can calculate terminator efficiency using nt, deltaG and LH directly without calculating the score first, ie : Efficiency = E(nt, deltaG,LH).</p> | ||
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<p>2. Modify the terminator sequence to match the user selected efficiency.</p> | <p>2. Modify the terminator sequence to match the user selected efficiency.</p> | ||
<p>Sometimes the user wants a terminator with specific efficiency. If the current efficiency of users terminator is not the one he want, our program can do mutation on terminator sequences and evolve a terminator that meets the requirement of efficiency. </p> | <p>Sometimes the user wants a terminator with specific efficiency. If the current efficiency of users terminator is not the one he want, our program can do mutation on terminator sequences and evolve a terminator that meets the requirement of efficiency. </p> | ||
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Revision as of 18:34, 26 September 2012
Future Version of Our Software
Introduction
Now our pc software and online tool can predict the efficiency of rho-independent terminator. The algorithm is based on two scoring systems, which were created by d'Aubenton Carafa and Elena A Lesnik respectively. The scoring systems were created to predict intrinsic terminators. So when we use them to predict terminator efficiency, the parameters of the score calculation may not be the best.What’s more, if the efficiency of their terminator is not suitable for users, they have to modify the terminator themselves. In the future, we want to solve these two problems.
Future Plan
1. Mutate the coefficients of the scoring formular to help get the best simulation formular of score and efficiency
D Score = nT * 18.16 + deltaG / LH * 96.59 – 116.87
(nT is the score of t tail, deltaG is the energy change of the stemloop formation and LH is the length of stemloop sequence.)
Here the coefficient of each terms can be adjusted to help make the best simulation between score and efficiency. Maybe we can treat efficiency as a function of those terms directly, which means we can calculate terminator efficiency using nt, deltaG and LH directly without calculating the score first, ie : Efficiency = E(nt, deltaG,LH).
2. Modify the terminator sequence to match the user selected efficiency.
Sometimes the user wants a terminator with specific efficiency. If the current efficiency of users terminator is not the one he want, our program can do mutation on terminator sequences and evolve a terminator that meets the requirement of efficiency.
