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.
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.
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.