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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.
