Team:SUSTC-Shenzhen-B/future plan

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                <h2>Introduction</h2>
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                <h3>Transcription:</h3>
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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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<p>The transcription stage, the reading of genetic information from DNA, is composed of promoter binding and the activation of RNA polymerase, RNA transcript initiation and promoter escape, RNA transcript elongation, and transcript termination, and release. </p>  
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                 <h3>What is terminator?</h3>
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<p>Terminators are genetic parts that usually occur at the end of a gene or operon and cause transcription to stop. In prokaryotes, terminators usually fall into two categories (1) rho-independent terminators and (2) rho-dependent terminators.</p>
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<h3><font face="Arial, Helvetica"><b><font color="#0000FF">Introduction</font></b></font></h3>
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<p>Rho-independent terminators are generally composed of palindromic sequence that forms a stem loop rich in G-C base pairs followed by several T bases. The conventional model of transcriptional termination is that the stem loop causes RNA polymerase to pause and transcription of the poly-A tail causes the RNA:DNA duplex to unwind and dissociate from RNA polymerase.
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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>Terminator Efficiency:</h3>
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<p>Although terminators are positioned at the ends of genes, they also play irreplaceable roles. It is important that transcription is imperfectly terminated at some terminator so that the ratio of the amount of the mRNA transcribed from upstream and that from downstream of the terminator is controlled. This regulation is qualified by the termination efficiency.</p>
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              <h3>Brief idea to calculate efficiency:</h3>
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<p>The fluorescence produced by the characterization devices are then measured using flow cytometry to calculate the termination efficiency of the terminators.</p>
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<p>E=S/(S+F)</p>
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<p>E: Terminator efficiency</p>
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<p>S: The number of cells that have been terminated successfully</p>
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<p>F: Number of cells that haven’t been terminated successfully.</p>
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<p>For more information about how to calculate the terminator efficiency, please see algorithm.</p>
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                <h2>Explanations</h2>
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<p>The process of transcription</p>
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<p>the secondary structure of terminator</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><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>Measurment</p>
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<p><font face="Arial, Helvetica, sans-serif">The formula of d  score calculation is :<br />
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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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  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><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="http://2012.igem.org/wiki/images/archive/0/0a/20120925123601%21Future_plan.1.JPG" class="img_fl img_border" />
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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.