# Team:SUSTC-Shenzhen-B/algorithm.1

(Difference between revisions)
 Revision as of 18:20, 26 September 2012 (view source)← Older edit Revision as of 02:33, 26 October 2012 (view source)Water (Talk | contribs) Newer edit → Line 1: Line 1: - {{tempalte:sustc_shenzhen_b/1}} - + - SUSTC iGEM Theme - Free CSS Template + - + - + + Title + + + + + - + -
+
-
+
- + -

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. [1] described TransTermHP, a new computational method to rapidly and accurately detect Rho-independent transcription terminators.

Line 18: Line 476:

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

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

(1)

(1)

-

where

where

(2)

(2)

-

for n=1...15 and  =1.

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:

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:

Line 30: Line 486:

Table 1

Table 1

Parameters used to evaluate hairpins

Parameters used to evaluate hairpins

-

Pairing   Energy

+

Pairing   Energy

-

G-C           -2.3

+

G-C             -2.3

-

A-T           -0.9

+

A-T             -0.9

-

G-T           1.3

+

G-T             1.3

-

Mismatch   3.5

+

Mismatch    3.5

-

Gap           6.0

+

Gap             6.0

Loop_pen(n)    1•(n - 2)

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.

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

- - - -
-

Reference

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.

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

+

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.

+ Read More +
+
+

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.

+ Read More +
+
+

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.

+ Read More +
+
+
-
+
-

Scoring Systems

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

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

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.