Simultaneous folding of alternative RNA structures with mutual constraints: an application to next-generation sequencing-based RNA structure probing.

Recent advances in next-generation sequencing technology have significantly promoted high-throughput experimental probing of RNA secondary structures. The resulting enzymatic or chemical probing information is then incorporated into a minimum free energy folding algorithm to predict more accurate RNA secondary structures. A drawback of this approach is that it does not consider the presence of alternative RNA structures. In addition, the alternative RNA structures may contaminate experimental probing information of each other and direct the minimum free-energy folding to a wrong direction. In this article, we present a combinatorial solution for this problem, where two alternative structures can be folded simultaneously given the experimental probing information regarding the mixture of these two alternative structures. We have tested our algorithm with artificially generated mixture probing data on adenine riboswitch and thiamine pyrophosphate (TPP) riboswitch. The experimental results show that our algorithm can successfully recover the ON and OFF structures of these riboswitches.