# Team:SUSTC-Shenzhen-B/algorithm

(Difference between revisions)
 Revision as of 18:32, 26 September 2012 (view source)← Older edit Latest revision as of 21:03, 26 October 2012 (view source)Water (Talk | contribs) (23 intermediate revisions not shown) Line 1: Line 1: - {{tempalte:sustc_shenzhen_b/1}} - + - SUSTC iGEM Theme - Free CSS Template + - + - + + Title + + + + + - + -
+
-
+
- + -

Overview

+ + + + + +
+
+
+ +
+

Algorithm Overview

TTEC is the first published software to predict terminator efficiency. It takes DNA sequences as input and returns the terminator efficiency value.

TTEC is the first published software to predict terminator efficiency. It takes DNA sequences as input and returns the terminator efficiency value.

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

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

-

1.Cut the input terminator sequence into three parts, A tail, stemloop and T tail.

+

1. Use RNA folding algorithm to predict the secondary structure of terminator and and recognize A tail, stemloop and T tail.

-

2.Score the terminator.

+

2. From the secondary structure, we calculate the free energy of stem loop, and generate a score by considering stem loop free energy and T tail

-

3.Calculate the efficiency of terminator using the formula created by our team.

+

3. From the score, we predict the terminator efficiency based on the score-terminator equation.

- + -
+

- + - + - + - + -

+

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.

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. 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. Thus we use it to help us cut the terminator into three parts.

From the table we can see that Elena A Lesnik Scoring System is totally energy based. 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. Thus we use it to help us cut the terminator into three parts.

-

+

- +
- + +
+ +
+
+
+
+

Kingsford Scoring System

+

In 2007, Carleton L Kingsford et al. described TransTermHP, a new computational software to rapidly and accurately detect Rho-independent transcription terminators.

+
+

Carafa Scoring System

+

Carafa Scoring System is created by d'Aubenton Carafa. The score of terminator consists of two parts,the free energy of stemloop and the score of 15 nt poly T tail.

+
+

Lesnik Scoring System

+

Lesnik Scoring System is created by Elena A Lesnik. The score is totally energy based,which includes the free energy change to form stemloop and RNA-DNA duplex.

+
+
+
+
+ - +
+
+ +
+
-
+
-

Scoring Systems

+ - + - + -
+ - + -
+ - + -
+ - + -
+ -
+
-
- + -
+ -
+
-
+
+ + +

Title

# Algorithm Overview

TTEC is the first published software to predict terminator efficiency. It takes DNA sequences as input and returns the terminator efficiency value.

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

1. Use RNA folding algorithm to predict the secondary structure of terminator and and recognize A tail, stemloop and T tail.

2. From the secondary structure, we calculate the free energy of stem loop, and generate a score by considering stem loop free energy and T tail

3. From the score, we predict the terminator efficiency based on the score-terminator equation.

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. 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. Thus we use it to help us cut the terminator into three parts.

## Kingsford Scoring System

In 2007, Carleton L Kingsford et al. described TransTermHP, a new computational software to rapidly and accurately detect Rho-independent transcription terminators.