Team:SUSTC-Shenzhen-B/achievements

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                 <h2>Achievements</h2>
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                 <h2><p>Achievements</p></h2>
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                 <h3 class="STYLE13">1. Function of our Web Tool and PC Software</h3>
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                <h3>Software</h3>
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<p>If the user input his terminator sequence, our program will output the secondary structure of the terminator based on Energy Minimization Rule and the termination efficiency.  There is a database we make which includes many efficiency-measured terminators and some basic information of those terminators.</p>
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<p>1. If users input the full sequence of terminator, our program can divide it into three parts, A tail, stemloop, and T tail.</p>
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<p>2. By using Free energy(or Hairpin Score) Minimization Rule, we can get secondary structure of stemloop. Then we can output a picture of the terminator.</p>
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<h3 class="STYLE13">2. Calculation of Terminator Efficiency</h3>
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<p>3. By using the efficiency data from lecture, database and a few our experiment results,we determined the parameters of our algorithm. However, because of the time limit, we have not finished to measure more than one hundred terminators to get the best fitting equation between score and terminator efficiency. So our future software version will perform better.</p>
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<p>We calculate the d score of terminators we got from Biofab.Terminator Library. Then we made a simulation formula of d score and termination efficiency based on the efficiency data in that terminator library and the score we calculated. We made linear fitting and the R^2 is 0.54. The picture below shows the results:</p><p>
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                <h3>Database</h3>
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<p>(Figure 1:The x-axis is d score and the y-axis is termination  efficiency)</p>
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<p>To build a complete rho-independent terminator system, we had to create a new terminator efficiency database which can make users choose the terminator they need more conveniently and easily. </p>
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<p>Our lab group did  experiments to measured efficiency of some terminators. We chose five of them  to see if the prediction of TTEC(the software we created to predict terminator efficiency) works well. The picture below shows the results. The x-axis is the  efficiency data of got from our experiments and the y-axis is the efficiency  predicted by TTEC. We can see that the slope of linear fitting is closed to 1  and the R^2 is 0.621.</p>
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<img src="https://static.igem.org/mediawiki/2012/3/33/%E6%97%A0%E6%A0%87%E9%A2%982.png" class="img_fl img_border" /></p>
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<p>(Figure 2)</p>
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<p>We thought the results were  good but we would continue to better our prediction in future.</p>
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<h3 class="STYLE13">3. Our Database</h3>
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<p>This is such a complete database that includes almost whole characters of terminators. Users can select terminator in different length, different efficiency, and different category from our database as long as they want. </p>
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<p>We built a database of terminators whose efficiency had been measured. Not only terminator efficiency , other information such as the direction, category and structure are also included. Some of the data were from partsregistry and Biofab.Terminator Library. Others were from papers. We read so many papers to find those terminators and some of the information were got through our e-mail with the author.The database will continue to update so it will be more useful for people. </p>
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<p>In our TE database, the structure formation of terminator is displayed. </p>
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<p><img src="https://static.igem.org/mediawiki/2012/0/0d/%E6%97%A0%E6%A0%87%E9%A2%9821.png" class="img_fl img_border" /></p>
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<p>The sources of terminator in our database are from the biobricks of partsregistry.org, papers we have read and database. And we selected part of whole terminators we had search which had been proved that they can work. What’s more, we offered every terminator’s efficiency.</p>
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                <h2>Hard Work</h2>
 
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Revision as of 00:06, 27 September 2012

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Achievements

1. Function of our Web Tool and PC Software

If the user input his terminator sequence, our program will output the secondary structure of the terminator based on Energy Minimization Rule and the termination efficiency. There is a database we make which includes many efficiency-measured terminators and some basic information of those terminators.

2. Calculation of Terminator Efficiency

We calculate the d score of terminators we got from Biofab.Terminator Library. Then we made a simulation formula of d score and termination efficiency based on the efficiency data in that terminator library and the score we calculated. We made linear fitting and the R^2 is 0.54. The picture below shows the results:


(Figure 1:The x-axis is d score and the y-axis is termination efficiency)

Our lab group did experiments to measured efficiency of some terminators. We chose five of them to see if the prediction of TTEC(the software we created to predict terminator efficiency) works well. The picture below shows the results. The x-axis is the efficiency data of got from our experiments and the y-axis is the efficiency predicted by TTEC. We can see that the slope of linear fitting is closed to 1 and the R^2 is 0.621.

(Figure 2)

We thought the results were good but we would continue to better our prediction in future.

3. Our Database

We built a database of terminators whose efficiency had been measured. Not only terminator efficiency , other information such as the direction, category and structure are also included. Some of the data were from partsregistry and Biofab.Terminator Library. Others were from papers. We read so many papers to find those terminators and some of the information were got through our e-mail with the author.The database will continue to update so it will be more useful for people.