A Knotty Problem
A pseudoknot is an RNA secondary structure formed by pairing between a loop and a region located outside of the stem flanking the loop. Pseudoknots fold into knot-shaped 3D conformation. The image below shows a simple pseudoknot structure found in human telomerase. https://en.wikipedia.org/wiki/Pseudoknot Pseudoknots are involved in a number of biological functions including gene expression and viral replication. Pseudoknots are known to exist in ribosomal RNA, viral RNA and a number of ribosomes. Pseudobase++ is probably the largest database of experimentally determined or predicted RNA sequences containing pseudoknots. Computational methods for predicting RNA secondary structures without pseudoknots have been around for quite some time. Among the more popular are Mfold , Sfold , and RNAstructure . A common method for predicting secondary structure is to use a thermodynamic energy model to find a structure with the minimum free energy, the MFE structure. A dynamic...