Analysis of RNA Pseudoknots with a Context-Sensitive Grammar
In this study, a context-sensitive grammar is suggested to analyze some patterns and configurations of RNA secondary structures. The use of context-sensitive grammar to analyze pseudoknots allows us to represent RNA structures more naturally comparing wit
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Abstract In this study, a context-sensitive grammar is suggested to analyze some patterns and configurations of RNA secondary structures. The use of context-sensitive grammar to analyze pseudoknots allows us to represent RNA structures more naturally comparing with a conventional approach of using Stochastic context-free grammar to model pseudoknots. The suggested technique directly reflects the characteristic appearance of several forms of RNA secondary structure, i.e., hairpins, internal loops, double helixes, and bulge loops. Keywords Context free grammar RNA sequence
Context-sensitive grammar Pseudoknots
1 Introduction 1.1
DNA and RNA
The DNA consists of sugar phosphate backbone on the outside of the helix and four nitrogenous bases on the inside of the double strand [1]. The ladder part, rung, is composed of two base pairs, adenosine (A)-thymine (T) pair and cytosine (C)guanine (G) pair. When the DNA is replicated into RNA, the helix is separated and matched into RNA as in Fig. 1. The process of making protein, which is called protein synthesis, consists of three stages, i.e., transcription, splicing, and translation. In the transcription phase, one DNA sequence is replicated to a complementary RNA which is called pre mRNA. In the splicing phase, the introns (the non-coding region) of the pre mRNA are removed, and the remaining exons (coding region) are connected together, which becomes mRNA. Today, the introns are believed to play some role to express
K.-Y. Sung (&) Handong Global University, Pohang, South Korea e-mail: [email protected] © Springer Science+Business Media Singapore 2016 J.J. (Jong Hyuk) Park et al. (eds.), Advanced Multimedia and Ubiquitous Engineering, Lecture Notes in Electrical Engineering 393, DOI 10.1007/978-981-10-1536-6_100
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Fig. 1 Double stranded DNA sequences and RNA
G---C---C----G---A----T---T----G---C---A---A The DNA Helix C---G---G----C---T----A---A----C---G---T----T
C---G---G----C---U----A---A----C---G---U----U
genes, which was regarded as junk in the early days [2]. The protein is synthesized in the translation phase by joining together amino acid encoded in the mRNA.
1.2
Pseudoknots and Context-Free Grammar
The recognition and prediction of RNA secondary structure, especially RNA pseudoknots, plays an important role in protein synthesis, e.g., ribosomal frameshifting, an infectious or tumor virus, a mutation of HIV, RNA-protein interaction, etc. [3]. Various forms of context-free grammars have been used to recognize and model RNA sequence [4]. Pseudoknots are tertiary RNA sequence consisting of base pairing between a secondary loop structure and complimentary bases outside the loop. Conventionally context-free grammars have been used to identify the secondary structure of RNA molecules from the given nucleotide sequence when we consider an RNA sequence as a string (or a valid sentence) of a programming language. There are typical types of pseudoknots, i.e., an interior loop, a bulge loop, a hairpin loop, and a helix. The context-free gramm
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