Team:SUSTC-Shenzhen-B/future plan

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                <h2>Future Version of Our Software</h2>
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        <a href="http://www.terminatorefficiency.com/software.aspx"><h2><p>Future Version of Our Software</a></p></h2>
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                 <h3>Introduction</h3>
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<p>Now our pc software and online tool can predict the efficiency of rho-independent terminator. There are two algorithms, algorithm 1 and algorithm 2, which are based on the model created by d'Aubenton Carafa and Elena A Lesnik respectively. But when users input the sequence of their terminator, they have to choose one of the algorithms without any idea of which one is better. What’s more, if the efficiency of their terminator is not suitable for them, they have to modify the terminator themselves. Thus, we want to solve these problems in the future.</p>  
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<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. In the future, we want to better predict the efficiency  of terminators using better formula and create a model of terminator efficiency prediction. What’s more, we hope we can do mutation on user’s  terminator sequence to give a derived terminator which meet the user’s requirement of efficiency.</p>
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                 <h3>Future Plan</h3>
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<p>1. Change the coefficient of the scoring formular and find the best algorithm</p>
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<h3><font face="Arial, Helvetica"><b><font color="#0000FF">Future Plan</font></b></font></h3>
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<p>D Score = nT * 18.16 + deltaG / LH * 96.59 – 116.87</p>
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<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>
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<p><font face="Arial, Helvetica"><strong>1. Mutate the coefficients of the scoring formular to help get the best simulation formular of score and  efficiency</strong></font></p>
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<p> Here the coefficient of each terms can be adjusted to help make the best simulation between score and efficiency. Similarly, the calculation of E Score can also be improved.</p>
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<p><font face="Arial, Helvetica, sans-serif">The formula of d  score calculation is ：<br />
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<p> What’s more, we want to find out which algorithm can better predict the efficiency based on our experiment data.Then users don’t need to hesitate to choose algorithm.</p>
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  D Score = nT * 18.16 + deltaG / LH * 96.59 – 116.87<br />
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  (nT is the score of t tail, deltaG is the energy change of the stemloop formation and LH is the length of stemloop sequence.)<br />
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<p>2. Modify the terminator sequence to match the user selected efficiency</p>
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  Here the coefficient of each terms can be adjusted to help make the best simulation between score and efficiency. We can even try to 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).</font></p>
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<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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                <img src="https://static.igem.org/mediawiki/2012/0/0a/Future_plan.1.JPG" class="img_fl img_border" />
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<p><font face="Arial, Helvetica"><strong>2. Create  a model of terminator efficiency prediction</strong></font></p>
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<p><font face="Arial, Helvetica, sans-serif">The score of terminator includes two parts, stemloop and  ttail. We can do some experiments to know how stemloop and ttail effect the  efficiency of terminators and then create a model of that. We’ve bought about  100 terminators sequences. These sequences are mutated in their stem，loop  or t tail. We will measure their efficiency and then analyze the experiment  data to find some regular pattern and create our own model.</font></p>
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<p><font face="Arial, Helvetica, sans-serif"><strong>3. Modify  the terminator sequence to match the user selected efficiency</strong></font></p>
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<font face="Arial, Helvetica, sans-serif">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.</font>
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    <img src="https://static.igem.org/mediawiki/2012/archive/0/0a/20120925123601%21Future_plan.1.JPG" class="img_fl img_border" />
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    <img src="https://static.igem.org/mediawiki/2012/6/67/Future_plan.2.JPG" class="img_fl img_border" /></font></p>
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Latest revision as of 03:35, 27 September 2012

SUSTC iGEM Theme - Free CSS Template

SUSTC iGEM Theme - Free CSS Template

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. In the future, we want to better predict the efficiency of terminators using better formula and create a model of terminator efficiency prediction. What’s more, we hope we can do mutation on user’s terminator sequence to give a derived terminator which meet the user’s requirement of efficiency.

Future Plan

1. Mutate the coefficients of the scoring formular to help get the best simulation formular of score and efficiency

The formula of d score calculation is ：
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. We can even try to 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. Create a model of terminator efficiency prediction

The score of terminator includes two parts, stemloop and ttail. We can do some experiments to know how stemloop and ttail effect the efficiency of terminators and then create a model of that. We’ve bought about 100 terminators sequences. These sequences are mutated in their stem，loop or t tail. We will measure their efficiency and then analyze the experiment data to find some regular pattern and create our own model.

3. 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.