# Team:SUSTC-Shenzhen-B/algorithm

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 Revision as of 14:48, 7 September 2012 (view source)Water (Talk | contribs) (Created page with "{{tempalte:sustc_shenzhen_b/1}} SUSTC iGEM Theme - Free CSS Template Introduction to scoring system 2

Introduction to scoring system 2

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Scoring System 2 is based on the model created by d'Aubenton Carafa.[1] The score of terminator consists of two parts, the free energy of stemloop and the score of 15 nt poly T tail. The free energy of stemloop is calculated using Loop Dependent Energy Rules[2]. The minimization of the free energy also determined the secondary structure of the stemloop. T tail score is calculated by the formula given by d’ Aubenton Carafa. +

Scoring System 2 is based on the model created by d'Aubenton Carafa.[1] The score of terminator consists of two parts, the free energy of stemloop and the score of 15 nt poly T tail. The free energy of stemloop is calculated using Loop Dependent Energy Rules[2]. The minimization of the free energy also determined the secondary structure of the stemloop. T tail score is calculated by the formula given by d’ Aubenton Carafa.

- Detailed Calculation of Score +

Detailed Calculation of Score

- 1. Some definitions[2] +

1. Some definitions[2]

- i. Closing Base Pair +

i. Closing Base Pair

- For an RNA sequence, we number it from 5’ to 3’ . If i < j and nucleotides ri and rj form a base pair,we denote it by i.j. We call base ri’ or base pair i’.j’ is accessible from i.j if i < i’ ( < j’ ) < j and if there is no other base pair k.l so that i < k < i’ ( < j’ ) < l < j. We denote the collection of base and base pair accessible from i.j by L(i,j). Then i.j is the closing base pair. Here “L” means loop. +

For an RNA sequence, we number it from 5’ to 3’ . If i < j and nucleotides ri and rj form a base pair,we denote it by i.j. We call base ri’ or base pair i’.j’ is accessible from i.j if i < i’ ( < j’ ) < j and if there is no other base pair k.l so that i < k < i’ ( < j’ ) < l < j. We denote the collection of base and base pair accessible from i.j by L(i,j). Then i.j is the closing base pair. Here “L” means loop.

- ii. n-loop +

ii. n-loop

- If the loop contain n – 1 base pairs, we denote it by n-loop. (Because there is a closing base pair, so we denote it by n-loop even though the closing base pair is not included in the loop.) +

If the loop contain n – 1 base pairs, we denote it by n-loop. (Because there is a closing base pair, so we denote it by n-loop even though the closing base pair is not included in the loop.)

- Here we can divide loops which may be formed in the terminator secondary structure into two kinds. +

Here we can divide loops which may be formed in the terminator secondary structure into two kinds.

- 1-loop : Hairpin loop(size of loop shouldn’t be smaller than 3) +

1-loop : Hairpin loop(size of loop shouldn’t be smaller than 3)

- 2-loop : Interior Loop(right strand size and left strand size are both bigger than 0.) +

2-loop : Interior Loop(right strand size and left strand size are both bigger than 0.)

- Buldge(Size of one strand is bigger than 0 and that of another strand is 0.) +

Buldge(Size of one strand is bigger than 0 and that of another strand is 0.)

- Stack(size of the loop is 0.) +

Stack(size of the loop is 0.)

- 2. Calculation of the Minimum Free Energy Change of Stemloop Formation[3] +

2. Calculation of the Minimum Free Energy Change of Stemloop Formation[3]

- Assume i.j is the closing base pair of the loop +

Assume i.j is the closing base pair of the loop

- G（i,j）= min { GH ( i , j ) , GS( i , j ) + G ( i + 1 , j – 1 ) , GBI( i , j ) } ; +

G（i,j）= min { GH ( i , j ) , GS( i , j ) + G ( i + 1 , j – 1 ) , GBI( i , j ) } ;

- GBI ( i , j ) = min{ gbi( i , j , k , l ) + G( k , l ) } for all  0 < k – i + l – j - 2 < max_size +

GBI ( i , j ) = min{ gbi( i , j , k , l ) + G( k , l ) } for all  0 < k – i + l – j - 2 < max_size

- G(i,j) is the minimum free energy change of stemloop formation. GH is the free energy change to form a hairpin loop. GS is the free energy change to form a stack. GBI is to calculate the minimum free energy change of structure containing 2-loop. gbi(i,j,k,l) is the free energy change to form 2-loop. +

G(i,j) is the minimum free energy change of stemloop formation. GH is the free energy change to form a hairpin loop. GS is the free energy change to form a stack. GBI is to calculate the minimum free energy change of structure containing 2-loop. gbi(i,j,k,l) is the free energy change to form 2-loop.

- 3.Calculation of T Tail Score +

3.Calculation of T Tail Score

- Here we consider 15 nucleotide in the downstream of stemloop. T tail score nT is calculated as follows : +

Here we consider 15 nucleotide in the downstream of stemloop. T tail score nT is calculated as follows :

- In our program, if the length of the T tail( n ) is less than 15, we will only consider n nucleotides. If TL is more than 15, we will only consider 15 nucleotides. +

In our program, if the length of the T tail( n ) is less than 15, we will only consider n nucleotides. If TL is more than 15, we will only consider 15 nucleotides.

- 4.Calculation of Score +

4.Calculation of Score

- Score = nT * 18.16 + deltaG / LH * 96.59 – 116.87 +

Score = nT * 18.16 + deltaG / LH * 96.59 – 116.87

- Here nT is T tail score. deltaG is the minimum free energy change of stemloop formation. LH is the length of stemloop. +

Here nT is T tail score. deltaG is the minimum free energy change of stemloop formation. LH is the length of stemloop.

## Revision as of 14:53, 7 September 2012

SUSTC iGEM Theme - Free CSS Template

SUSTC iGEM Theme - Free CSS Template

## Introduction to Scoring Systems

### Introduction to scoring system 2

Scoring System 2 is based on the model created by d'Aubenton Carafa.[1] The score of terminator consists of two parts, the free energy of stemloop and the score of 15 nt poly T tail. The free energy of stemloop is calculated using Loop Dependent Energy Rules[2]. The minimization of the free energy also determined the secondary structure of the stemloop. T tail score is calculated by the formula given by d’ Aubenton Carafa.

Detailed Calculation of Score

1. Some definitions[2]

i. Closing Base Pair

For an RNA sequence, we number it from 5’ to 3’ . If i < j and nucleotides ri and rj form a base pair,we denote it by i.j. We call base ri’ or base pair i’.j’ is accessible from i.j if i < i’ ( < j’ ) < j and if there is no other base pair k.l so that i < k < i’ ( < j’ ) < l < j. We denote the collection of base and base pair accessible from i.j by L(i,j). Then i.j is the closing base pair. Here “L” means loop.

ii. n-loop

If the loop contain n – 1 base pairs, we denote it by n-loop. (Because there is a closing base pair, so we denote it by n-loop even though the closing base pair is not included in the loop.)

Here we can divide loops which may be formed in the terminator secondary structure into two kinds.

1-loop : Hairpin loop(size of loop shouldn’t be smaller than 3)

2-loop : Interior Loop(right strand size and left strand size are both bigger than 0.)

Buldge(Size of one strand is bigger than 0 and that of another strand is 0.)

Stack(size of the loop is 0.)

2. Calculation of the Minimum Free Energy Change of Stemloop Formation[3]

Assume i.j is the closing base pair of the loop

G（i,j）= min { GH ( i , j ) , GS( i , j ) + G ( i + 1 , j – 1 ) , GBI( i , j ) } ;

GBI ( i , j ) = min{ gbi( i , j , k , l ) + G( k , l ) } for all 0 < k – i + l – j - 2 < max_size

G(i,j) is the minimum free energy change of stemloop formation. GH is the free energy change to form a hairpin loop. GS is the free energy change to form a stack. GBI is to calculate the minimum free energy change of structure containing 2-loop. gbi(i,j,k,l) is the free energy change to form 2-loop.

3.Calculation of T Tail Score

Here we consider 15 nucleotide in the downstream of stemloop. T tail score nT is calculated as follows :

In our program, if the length of the T tail( n ) is less than 15, we will only consider n nucleotides. If TL is more than 15, we will only consider 15 nucleotides.

4.Calculation of Score

Score = nT * 18.16 + deltaG / LH * 96.59 – 116.87

Here nT is T tail score. deltaG is the minimum free energy change of stemloop formation. LH is the length of stemloop.