WELL-DETERMINED REGIONS IN RNA SECONDARY STRUCTURE PREDICTION - ANALYSIS OF SMALL-SUBUNIT RIBOSOMAL-RNA

Recent structural analyses of genomic RNAs from RNA coliphages suggest that both well-determined base paired helices and well-determined str uctural domains that are identified by 'energy dot plot' analysis usin g the RNA folding package mfold, are likely to be predicted correctly To test these observations with another group of large RNAs, we have a nalyzed 15 ribosomal RNAs. Published secondary structure models that w ere derived by comparative sequence analysis were used to evaluate the predicted structures. Both the optimal predicted fold and the predict ed 'energy dot plot' of each sequence were examined, Each prediction w as obtained from a single computer run on an entire ribosomal RNA sequ ence, All predicted base pairs in optimal foldings were examined for a greement with proven base pairs in the comparative models, Our analyse s show that the overall correspondence. between the predicted and comp arative models varies for different RNAs and ranges from a low of 27% to a high of 70%, with a mean value of 49%, The correspondence improve s to a mean value of 81% when the analysis is limited to well-determin ed helices, In addition to well-determined helices, large well-determi ned structural domains can be observed in 'energy dot plots' of some 1 6S ribosomal RNAs, The predicted domains correspond closely with struc tural domains that are found by the comparative method in the same RNA s, Our analyses also show that measuring the agreement between predict ed and comparative secondary structure models underestimates the relia bility of structural prediction by mfold.