Team:SUSTC-Shenzhen-B/algorithm.1

(Difference between revisions)
 Revision as of 14:01, 26 October 2012 (view source)Water (Talk | contribs)← Older edit Latest revision as of 14:51, 26 October 2012 (view source) (One intermediate revision not shown) Line 396: Line 396:
• Home
• Home
• Project Overview
• Project Overview
• -
• Software +
• Software
-
• Overview
• +
• Overview
• Algorithm
• Algorithm
• Achievements
• Achievements
• Line 503: Line 503:

Kingsford Scoring System

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.

+

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

-

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.

+

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

-

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.

+

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.

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.