next up previous contents
Next: RNA16A model Up: Base-paired substitution models implemented Previous: RNA7A model   Contents

RNA7D model (Tillier, 98)

The RNA7D model (Tillier and Collins, 1998) is a biologically plausible restriction of the RNA7A model. The restictions in the 7D model are analogous to the restrictions made in the 6B. There is one more frequency parameter for the mismatch state and one more rate ratio parameter for the substitution rates involving this state. The reference for the rate ratios are the rate of double transitions. This model is described by the following rate matrix (table 2.9).

Table 2.9: RNA7D transition matrix
Q = m_r \times \left(
...pha_3 & \pi_{CG}\alpha_3 & * \\

Gowri-Shankar Vivek 2003-04-24