BJRNAFold: Prediction of RNA Secondary Structure Base on Constraint Parameters

Predicting RNA secondary structure as accurately as possible is very important in functional analysis of RNA molecules. However, different prediction methods and related parameters including terminal GU pair of helices, minimum length of helices, and free energy systems often give different prediction results for the same RNA sequence. Then, which structure is more important than the others? i.e. which combinations of the methods and related parameters are the optimal? In order to investigate above problems, first, three prediction methods, namely, random stacking of helical regions (RS), helical regions distribution (HD), and Zuker's minimum free energy algorithm (ZMFE) were compared by taking 1139 tRNA sequences from Rfam database as the samples with different combinations of parameters. The optimal parameters are derived. Second, Zuker's dynamic programming method for prediction of RNA secondary structure was revised using the above optimal parameters and related software BJRNAFold was developed. Third, the effects of short-range interaction were studied. The results indicated that the prediction accuracy would be improved much if proper short-range factor were introduced. But the optimal short-range factor was difficult to determine. A user-adjustable parameter for short-range factor was introduced in BJRNAFold software.