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           <div class="box">
           <div class="box">
                       <h2>Kingsford Scoring System</h2>
                       <h2>Kingsford Scoring System</h2>
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                       <p>In 2007, Carleton L Kingsford et al. [1] described TransTermHP, a new computational method to rapidly and accurately detect Rho-independent transcription terminators.</p>
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                       <p>In 2007, Carleton L Kingsford et al. described TransTermHP, a new computational software to rapidly and accurately detect Rho-independent transcription terminators.</p>
                       <a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B/algorithm.1">Read More</a>
                       <a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B/algorithm.1">Read More</a>
                     </div>
                     </div>
                     <div class="box">
                     <div class="box">
                       <h2>Carafa Scoring System</h2>
                       <h2>Carafa Scoring System</h2>
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                       <p>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.</p>
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                       <p>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.</p>
                       <a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B/algorithm.2">Read More</a>
                       <a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B/algorithm.2">Read More</a>
                     </div>
                     </div>
                     <div class="box last">
                     <div class="box last">
                       <h2>Lesnik Scoring System</h2>
                       <h2>Lesnik Scoring System</h2>
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                       <p>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.</p>
                       <a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B/algorithm.3">Read More</a>
                       <a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B/algorithm.3">Read More</a>
                     </div>
                     </div>

Latest revision as of 14:51, 26 October 2012

Title

Kingsford Scoring System

In 2007, Carleton L Kingsford et al. [1] described TransTermHP, a new computational method to rapidly and accurately detect Rho-independent transcription terminators.

They put forward an algorithm to predict Rho-independent terminators.

The first 15 bases of the potential tail sequence are scored using a function:

(1)

where


(2)

for n=1...15 and =1.

The energy of potential hairpin configurations adjacent to a reference position can be found efficiently with a dynamic programming algorithm. The table entry hairpin_score[i,j] gives the cost of the best hairpin structure for which the base of the 5' stem is at nucleotide position i and the base of the 3' stem is at position j. The entry hairpin_score[i,j] can be computed recursively as follows:

(3)

The function energy(i,j) gives the cost of pairing the nucleotide at i with that at j, and loop_pen(n) gives the cost of a hairpin loop of length n. The hairpin's loop is forced to have a length between 3 and 13 nt, inclusive, by setting loop_pen(n) to a large constant for any n outside that range. The constant 'gap' gives the cost of not pairing a base with some base on the opposite stem and thus introducing a gap on one side of the hairpin stem.

Table 1

Parameters used to evaluate hairpins

Pairing Energy

G-C -2.3

A-T -0.9

G-T 1.3

Mismatch 3.5

Gap 6.0

Loop_pen(n) 1•(n - 2)

Parameters used to evaluate the energy of a potential hairpin where n is the length of the hairpin loop.

Reference

1. Carleton L Kingsford, Kunmi Ayanbule and Steven L Salzberg: Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake. Genome Biology 2007, 8:R22.


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.

Read More

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.

Read More

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.

Read More
South University of Science and Technology of China