Lost in folding space? Comparing four variants of the thermodynamic model for RNA secondary structure prediction

BMC Bioinformatics

Table 3 Cross-reference between the energy functions in our programs, and which energy contributions (model functions) they call upon.

This table shows the use of the very same energy functions for all grammars. Energy differences only stem from different combinations. In the first column, we list the energy model functions. The next four columns contain the evaluation functions of the four grammars.
To retrieve the energy of the example structure of Figure 1 for NoDangle, you should read the table like this: The first evaluation function of the structure is sr. Look for all rows in column two where sr appears. It is just the case for sr _energy. Next is bl, which again shows up in the row for sr _energy but also for bl _energy. The concrete energy values depend on the concrete input bases, thus one should understand the model functions as table look-ups with the bases as parameters. The energy of the whole structure is just the sum of all local energy contributions.
Some evaluation functions do not use model functions. The four variants of the evaluation function cadd and combine just add energies from their left and right substructures. Trafo and incl do not change the energy value at all and nil simply returns 0.

ISSN: 1471-2105