Image source: http://www.cbs.dtu.dk/~gorodkin/appl/slogo.html
A formal covariance model, COVE, was devised by Eddy and Durbin. The model provides very accurate results, but is extremely slow and unsuitable for large genomes. Stochastic Context Free Grammars (SCFGs) have also been used to model RNA secondary structure. Examples of these are tRNAScan-SE, and a program created to find snoRNAs. Typically, with SCFG approaches, the grammars are created by using a training set of data, and then the grammars are applied to potential sequences to see if they fit into the language. SCFGs allow the detection of sequences belonging to a family, such as tRNAs, group I introns, snoRNAs, snRNAs, etc. With a SCFG approach, base-paired columns are modeled by pairwise emitting non terminals (for example aWu) while single-stranded columns are modeled by leftwise emitting nonterminals (such as gW), when possible. Any RNA structure can then be reduced to a SCFG (see Durbin, et al., p 278-279). Tranformational Grammars Transformational grammars were first described by the linguist Noam Chomsky in the 1950’s. (Yes, this is the same Noam Chomsky who has expressed various dissident