CCG-Based RNA Secondary Structure Prediction
نویسندگان
چکیده
Various systems have been proposed to predict secondary structures of RNAs using their sequence information. Among them, Uemura et al. [2] described a system that recognizes some typical RNA secondary structures such as hairpin loops and pseudoknots with Tree Adjoining Grammar. However, their work captures only known sub-structures, and not those unknown sub-structures that might also exist. Ternary pseudoknot, composed of three pairs of cross-serially arranged reverse-complementary sequences, may be one such example. Figure 1 illustrates an example ternary pseudoknot. We describe a version of Combinatory Categorial Grammars (CCGs) for an RNA secondary prediction system to discover such unknown sub-structures. The parser for the proposed CCG takes an RNA sequence and produces the semantics string that contains structural information of the sequence.
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