Abstract
The RNA pseudoknot has been proposed as a significant structural motif in a wide range of biological processes of RNAs. A pseudoknot involves intramolecular pairing of bases in a hairpin loop with bases outside the stem of the loop to form a second stem and loop region. In this study, we propose a method for searching and predicting pseudoknots that are likely to have functional meaning. In our procedure, the orthodox hairpin structure involved in the pseudoknot is required to be both statistically significant and relatively stable to the others in the sequence. The bases outside the stem of the hairpin loop in the predicted pseudoknot are not entangled with any formation of a highly stable secondary structure in the sequence. Also, the predicted pseudoknot is significantly more stable than those that can be formed from a large set of scrambled sequences under the assumption that the energy contribution from a pseudoknot is proportional to the size of second loop region and planar energy contribution from second stem region. A number of functional pseudoknots that have been reported before can be identified and predicted from their sequences by our method.