International Science Index

3
10007311
CompPSA: A Component-Based Pairwise RNA Secondary Structure Alignment Algorithm
Abstract:
The biological function of an RNA molecule depends on its structure. The objective of the alignment is finding the homology between two or more RNA secondary structures. Knowing the common functionalities between two RNA structures allows a better understanding and a discovery of other relationships between them. Besides, identifying non-coding RNAs -that is not translated into a protein- is a popular application in which RNA structural alignment is the first step A few methods for RNA structure-to-structure alignment have been developed. Most of these methods are partial structure-to-structure, sequence-to-structure, or structure-to-sequence alignment. Less attention is given in the literature to the use of efficient RNA structure representation and the structure-to-structure alignment methods are lacking. In this paper, we introduce an O(N2) Component-based Pairwise RNA Structure Alignment (CompPSA) algorithm, where structures are given as a component-based representation and where N is the maximum number of components in the two structures. The proposed algorithm compares the two RNA secondary structures based on their weighted component features rather than on their base-pair details. Extensive experiments are conducted illustrating the efficiency of the CompPSA algorithm when compared to other approaches and on different real and simulated datasets. The CompPSA algorithm shows an accurate similarity measure between components. The algorithm gives the flexibility for the user to align the two RNA structures based on their weighted features (position, full length, and/or stem length). Moreover, the algorithm proves scalability and efficiency in time and memory performance.
Paper Detail
63
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2
12151
Predicting the Minimum Free Energy RNA Secondary Structures using Harmony Search Algorithm
Abstract:

The physical methods for RNA secondary structure prediction are time consuming and expensive, thus methods for computational prediction will be a proper alternative. Various algorithms have been used for RNA structure prediction including dynamic programming and metaheuristic algorithms. Musician's behaviorinspired harmony search is a recently developed metaheuristic algorithm which has been successful in a wide variety of complex optimization problems. This paper proposes a harmony search algorithm (HSRNAFold) to find RNA secondary structure with minimum free energy and similar to the native structure. HSRNAFold is compared with dynamic programming benchmark mfold and metaheuristic algorithms (RnaPredict, SetPSO and HelixPSO). The results showed that HSRNAFold is comparable to mfold and better than metaheuristics in finding the minimum free energies and the number of correct base pairs.

Paper Detail
1268
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1
9393
Maximum Common Substructure Extraction in RNA Secondary Structures Using Clique Detection Approach
Authors:
Abstract:
The similarity comparison of RNA secondary structures is important in studying the functions of RNAs. In recent years, most existing tools represent the secondary structures by tree-based presentation and calculate the similarity by tree alignment distance. Different to previous approaches, we propose a new method based on maximum clique detection algorithm to extract the maximum common structural elements in compared RNA secondary structures. A new graph-based similarity measurement and maximum common subgraph detection procedures for comparing purely RNA secondary structures is introduced. Given two RNA secondary structures, the proposed algorithm consists of a process to determine the score of the structural similarity, followed by comparing vertices labelling, the labelled edges and the exact degree of each vertex. The proposed algorithm also consists of a process to extract the common structural elements between compared secondary structures based on a proposed maximum clique detection of the problem. This graph-based model also can work with NC-IUB code to perform the pattern-based searching. Therefore, it can be used to identify functional RNA motifs from database or to extract common substructures between complex RNA secondary structures. We have proved the performance of this proposed algorithm by experimental results. It provides a new idea of comparing RNA secondary structures. This tool is helpful to those who are interested in structural bioinformatics.
Paper Detail
880
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