Table 7

Free energy parameters for internal loops.

Parameter

Explanation

Values


ΔG-length-I(n)

Destabilizing energy of internal loop of size n (n = 4, 5, 6,...)

1.7, 1.8, 2.0,...

ΔG-length-B(n)

Destabilizing energy of bulge of size n (n = 1, 2, 3,...)

3.8, 2.8, 3.2,...

ΔG-Internal-n (si, sj, si+1, sj-1)

Terminal mismatch free energy of closing base pair (si·sj) and neighbouring free bases si+1 and sj-1

-1.1, -0.7, -0.4, 0.0 and 0.7

ΔG-Asymmetry(l1, l2)

Penalty for asymmetric internal loops

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Aguirre-Hernández et al. BMC Bioinformatics 2007 8:34   doi:10.1186/1471-2105-8-34

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