ABSTRACT
Most viruses have RNA genomes, their biological functions are expressed more by folded architecture than by sequence
Among the various RNA structures, pseudoknots are the most typical. In general, RNA secondary structures prediction doesn't contain pseudoknots because of its difficulty in modeling
Here we present an algorithm of dynamic matching to predict RNA secondary structures with pseudoknots by combining the merits of comparative and thermodynamic approaches
We have tested and verified our algorithm on some viral RNA
Comparisons show that our algorithm and loop matching method has similar accuracy and time complexity, and are more sensitive than the maximum weighted matching method and Rivas algorithm. Among the four methods, our algorithm has the best prediction specificity. The results show that our algorithm is more reliable and efficient than the other methods