Genome-Wide Search for Pseudoknotted Noncoding RNA: A Comparative Study

Noncoding RNAs (ncRNAs) are functional RNA molecules, which are involved in many biological processes including gene regulation, chromosome replication, and RNA modification. There are two tools, RNA via tree decomposition (RNATOPS) and inference of RNA alignment (Infernal), which are capable of performing genome-wide pseudoknotted ncRNA search. This chapter conducts a comparative study on RNATOPS and Infernal. It analyzes and compares the performances of the two tools with respect to their ncRNA detection accuracies. The chapter presents some background materials related to this study. It describes the methodology used in the analysis of pseudoknotted ncRNA search, and also presents some experimental results and an interpretation of these results. It was observed that RNATOPS detected ncRNAs with less computation time than Infernal due to the filter functions incorporated in the RNATOPS tool. On the other hand, Infernal yields more hits than RNATOPS.