Pairwise RNA Pseudoknotted Structure Prediction Based on Stochastic Grammar
نویسندگان
چکیده
RNA secondary structure prediction is one of the major topics in bioinformatics. A prediction method based on a parsing algorithm for formal grammars is a promising approach. Also, it is expected that comparative sequence analysis achieves higher accuracy than the one using a single sequence since the former approach can use evolutionary information that homologous RNAs are likely to conserve a common structure. In this paper, we propose a prediction method using Pair-SMCFG (stochastic multiple context-free grammar) based on comparative sequence analysis and show experimental results on structure prediction by the method.
منابع مشابه
Stochastic modeling of RNA pseudoknotted structures: a grammatical approach
MOTIVATION Modeling RNA pseudoknotted structures remains challenging. Methods have previously been developed to model RNA stem-loops successfully using stochastic context-free grammars (SCFG) adapted from computational linguistics; however, the additional complexity of pseudoknots has made modeling them more difficult. Formally a context-sensitive grammar is required, which would impose a large...
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