DCJ-RNA - double cut and join for RNA secondary structures

Ghada H Badr,Haifa A Al-Aqel

doi:10.1186/s12859-017-1830-6

Abstract

BackgroundGenome rearrangements are essential processes for evolution and are responsible for existing varieties of genome architectures. Many studies have been conducted to obtain an algorithm that identifies the minimum number of inversions that are necessary to transform one genome into another; this allows for genome sequence representation in polynomial time. Studies have not been conducted on the topic of rearranging a genome when it is represented as a secondary structure. Unlike sequences, the secondary structure preserves the functionality of the genome. Sequences can be different, but they all share the same structure and, therefore, the same functionality.ResultsThis paper proposes a double cut and join for RNA secondary structures (DCJ-RNA) algorithm. This algorithm allows for the description of evolutionary scenarios that are based on secondary structures rather than sequences. The main aim of this paper is to suggest an efficient algorithm that can help researchers compare two ribonucleic acid (RNA) secondary structures based on rearrangement operations. The results, which are based on real datasets, show that the algorithm is able to count the minimum number of rearrangement operations, as well as to report an optimum scenario that can increase the similarity between the two structures.ConclusionThe algorithm calculates the distance between structures and reports a scenario based on the minimum rearrangement operations required to make the given structure similar to the other. DCJ-RNA can also be used to measure the distance between the two structures. This can help identify the common functionalities between different species.

Highlights

Genome rearrangements are essential processes for evolution and are responsible for existing varieties of genome architectures
We propose a double cut and join (DCJ)-ribonucleic acid (RNA) rearrangement algorithm and explain it in detail
DCJ-RNA algorithm The RNA component-based rearrangement algorithm uses a component-based representation [2] that allows for the unique description of any RNA pattern and shows the main features of the pattern efficiently

Summary

Introduction

Genome rearrangements are essential processes for evolution and are responsible for existing varieties of genome architectures. Many studies have been conducted to obtain an algorithm that identifies the minimum number of inversions that are necessary to transform one genome into another; this allows for genome sequence representation in polynomial time. Studies have not been conducted on the topic of rearranging a genome when it is represented as a secondary structure. The secondary structure preserves the functionality of the genome. RNA is responsible for transferring the genetic code from the nucleus to the ribosome to build proteins. It is identified as a series of letters with bases {A, C, G, U}. RNA’s secondary structure is required to define the functionality of RNA molecules.

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