GCG: The Analysis of RNA Secondary Structure

The prediction of RNA secondary structure differs significantly from that of protein secondary structure. The latter is based on crystallographic data, and by using a variety of empiric or semiempiric parameters, a prediction is achieved. RNA secondary structure prediction, on the other hand, is based on an energy calculation. Each nucleotide sequence can be calculated using a table of energies for stacking and loop destabilizing energies. The GCG program (1 ) foldrna is the program of M. Zuker (2 ), using the energies published by Turner (3 ). The algorithm and its usage are explained in Chapter 23 in Part II. This chapter shows the use of the foldrna program as implemented in the GCG package, including the broad range of output visualization provided.