Integration of RNA search methods for identifying novel riboswitch patterns in eukaryotes

Riboswitches are RNA genetic control elements that were recently discovered in living cells. To regulate gene expression, they utilize a unique mechanism whereby small molecules bind to the aptamer or box region causing a conformational switch, without the participation of proteins. Riboswitches were initially found in the 5' UTR of bacteria, with successive discoveries in prokaryotes. Evidence for their existence in eukaryotes has prompted their scarce detection in that kingdom. Bioinformatics methods are needed in order to locate new riboswitch candidates. Several relevant search strategies have been developed and investigated, each having its own advantages and deficiencies. By-merging several of these methods and integrating them in a hierarchical manner, it is possible to develop a combined strategy that will successfully locate potential candidates for the purpose of experimental validation.