# Team:SUSTC-Shenzhen-B/future plan

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 Revision as of 18:07, 23 September 2012 (view source)Water (Talk | contribs)← Older edit Revision as of 11:26, 25 September 2012 (view source)Water (Talk | contribs) Newer edit → Line 9: Line 9: +
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Future Version of Our Software

Future Version of Our Software

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Introduction

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Introduction

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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.

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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.

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Future Plan

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Future Plan

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

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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

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.)

(nT is the score of t tail, deltaG is the energy change of the stemloop formation and LH is the length of stemloop sequence.)

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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.

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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).

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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.

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2. Modify the terminator sequence to match the user selected efficiency

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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.

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.

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## Revision as of 11:26, 25 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. 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.