Team:SUSTC-Shenzhen-B/algorithm

From 2012.igem.org

(Difference between revisions)
Line 34: Line 34:
                 <h2>Classes </h2>
                 <h2>Classes </h2>
                 <ul class="tmo_ul_list">
                 <ul class="tmo_ul_list">
 +
 +
                    <li><a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B/algorithm">Overview</a></li>
                     <li><a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B/algorithm.1">Algorithm 1</a></li>
                     <li><a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B/algorithm.1">Algorithm 1</a></li>
                     <li><a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B/algorithm.2">Algorithm 2</a></li>
                     <li><a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B/algorithm.2">Algorithm 2</a></li>

Revision as of 18:57, 23 September 2012

SUSTC iGEM Theme - Free CSS Template

SUSTC iGEM Theme - Free CSS Template

Overview of Our Algorithm

Our team created a pc software and an online tool to help users calculate the efficiency of their terminators.

To calculate the efficiency of terminator efficiency, there are three steps.

First,we cut the input terminator sequence into three parts, including A tail, stemloop, T tail using Carleton L Kingsford Scoring System (Scoring System 1).

Next, we score the terminator based on the d'Aubenton Carafa Scoring System(Scoring System 2) or Elena A Lesnik Scoring System(Scoring System 3).

Finally, we calculate the efficiency of terminator using the simulation formular created by our team.

From the picture below we can see that there are two choices when scoring terminators. So there are two algorithms of our software.

Three scoring systems mentioned above were all created by researchers to predict rho-independent transcription terminators. If the score of a sequence is good, it is more likely to be a terminator sequence. The score of terminator consists of two parts, corresponding to stemloop and T tail. Here we made a table to show the similarity and difference of these three scoring systems.

From the table we can see that Elena A Lesnik Scoring System is totally energy based. But to calculate free energy we need many thermal parameters. Carleton L Kingsford Scoring System is simple and convenient to use because it doesn’t need to use such many thermal parameters. So we use it to help us cut the terminator into three parts, a tail, stemloop and t tail and use the rest two scoring systems to help get the efficiency of terminator. In fact, Carleton L Kingsford Scoring System can also be used to help calculate the efficiency. But we thought energy based scoring systems would be better to describe the terminator because energy was a basic concept when describing things. So we choose the rest two scoring systems to get efficiency.

The simulation formular of score and efficiency were made based on our experiment data.