# Team:SUSTC-Shenzhen-B/algorithm.2

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Carafa Scoring System

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Carafa Scoring System

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

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1. Some definitions[2]

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1. Some definitions[2]

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i. Closing Base Pair

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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.

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ii. n-loop

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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.

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

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

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

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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.)

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[5] Biochemistry 1995,34, 1121 1-1 1216  “Thermodynamic Parameters To Predict Stability of RNA-DNA Hybrid Duplexes”

[5] Biochemistry 1995,34, 1121 1-1 1216  “Thermodynamic Parameters To Predict Stability of RNA-DNA Hybrid Duplexes”

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Kingsford Scoring System

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Carafa Scoring System

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Lesnik Scoring System

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Scoring Systems

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Title

## Carafa Scoring System

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.

[1] J. Mol. Biol. (1990) 216, 835-858 “Prediction of Rho-independent Escherichia coli Transcription Terminators A Statistical Analysis of their RNA Stem-Loop Structures”

[2] Manual of Mfold Version 3.5

[3] http://unafold.math.rpi.edu/lectures/old_RNAfold/node2.html

[4]Nucl. Acids Res.-2001-Lesnik-3583-94 “Prediction of Rho-independent Escherichia coli ”

[5] Biochemistry 1995,34, 1121 1-1 1216 “Thermodynamic Parameters To Predict Stability of RNA-DNA Hybrid Duplexes”

## Kingsford Scoring System

Nunc tortor ante, accumsan vel malesuada vulputate, tempus quis dolor. In ut purus nulla. Etiam tincidunt pharetra metus eget ultricies. Integer mi ante, laoreet cursus.