pknotsRG: RNA pseudoknot folding including near-optimal structures and sliding windows

Reeder, Jens; Steffen, Peter; Giegerich, Robert

RNA pseudoknots play an important role in many biological processes. They build the catalytic core of some ribozymes (1, 2) and are an important building block of many structural RNAs. Pseudoknots are involved in telomerase activity (3) and they stimulate efficient programmed -1 ribosomal frameshifting (-1 PRF), a mechanism used by a wide range of RNA viruses to encode two proteins within one genomic region. In a recent study (4) over a thousand of potential -1 PRF signals were detected in the yeast genome. The majority of signals however seem to direct the ribosome to premature termination codons. This suggests a mechanism of post-transcriptional gene regulation through the nonsense-mediated mRNA decay pathway. Further genome wide studies have to elucidate this phenomenon. This and many more applications require fast RNA folding algorithms, that are also capable of folding pseudoknots.