Evaluate structure hypothesis

Hypotheses about an RNA structure can be tested using CLC Genomics Workbench. A structure hypothesis H is formulated using the structural constraint annotations described in Specifying structure constraints. By adding several annotations complex structural hypotheses can be formulated (see 23.21).

Given the set S of all possible structures, only a subset of these $ S_H$ will comply with the formulated hypotheses. We can now find the probability of H as:

$\displaystyle P(H) = \frac{\displaystyle\sum_{{s_H} \in {S_H}}{P(s_H)}}{\displaystyle\sum_{s \in S}{P(s)}} = \frac{PF_{H}}{PF_{{\rm {full}}}},$

where $ PF_{H}$ is the partition function calculated for all structures permissible by H $ (S_H)$ and $ PF_{\rm {full}}$ is the full partition function. Calculating the probability can thus be done with two passes of the partition function calculation, one with structural constraints, and one without. 23.21.

Image constraintannotations
Figure 23.21: Two constraints defining a structural hypothesis.