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
Evaluate structure hypothesis
Given the set S of all possible structures, only a subset of these will comply with the formulated hypotheses. We can now find the probability of H as:
where is the partition function calculated for all structures permissible by H and 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. 22.21.
Figure 22.21: Two constraints defining a structural hypothesis.