Team:SUSTC-Shenzhen-B/future plan

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                 <h2>Future Version of Our Software</h2>
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                 <h2>Introduction</h2>
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                <h3>Transcription：</h3>
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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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                 <h3>Introduction</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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<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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<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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                <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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<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> 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> 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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<p>2. Modify the terminator sequence to match the user selected efficiency</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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               <h3>Terminator Efficiency：</h3>
               <h3>Terminator Efficiency：</h3>

Revision as of 04:00, 23 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. 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.


Future Plan

1. Change the coefficient of the scoring formular and find the best algorithm

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. Similarly, the calculation of E Score can also be improved.

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.

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.


Terminator Efficiency：

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.


Brief idea to calculate efficiency:

The fluorescence produced by the characterization devices are then measured using flow cytometry to calculate the termination efficiency of the terminators.

E=S/(S+F)

E: Terminator efficiency

S: The number of cells that have been terminated successfully

F: Number of cells that haven’t been terminated successfully.

For more information about how to calculate the terminator efficiency, please see algorithm.

Explanations

The process of transcription


the secondary structure of terminator








Measurment


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