PreRkTAG: Prediction of RNA Knotted Structures Using Tree Adjoining Grammars

Abstract

Background: RNA molecules play many important regulatory, catalytic and structural roles in the cell, and RNA secondary structure prediction with pseudoknots is one the most important problems in biology. An RNA pseudoknot is an element of the RNA sec ondary structure in which bases of a single-stranded loop pair with complementary bases outside the loop. Modeling these nested structures (pseudoknots) causes numerous com putational diffilties and so it has been generally neglected in RNA structure prediction algorithms. Objectives: In this study, we present a new heuristic algorithm for the Prediction of RNA Knotted structures using Tree Adjoining Grammars (named PreRKTAG). Materials and Methods: For a given RNA sequence, PreRKTAG uses a genetic algorithm on tree adjoining grammars to propose a structure with minimum thermodynamic energy. The genetic algorithm employs a subclass of tree adjoining grammars as individuals by which the secondary structure of RNAs are modeled. Upon the tree adjoining grammars, new crossover and mutation operations were designed.The finess function is defied ac cording to the RNA thermodynamic energy function, which causes the algorithm conver gence to be a stable structure. Results: The applicability of our algorithm is demonstrated by comparing its iresults with three well-known RNA secondary structure prediction algorithms that support crossed structures. Conclusions: We performed our comparison on a set of RNA sequences from the RNAseP database, where the outcomes show effiency and practicality of the proposed algorithm.