Prediction of common secondary structures of RNAs: a genetic algorithm approach
- 15 February 2000
- journal article
- Published by Oxford University Press (OUP) in Nucleic Acids Research
- Vol. 28 (4), 991-999
- https://doi.org/10.1093/nar/28.4.991
Abstract
In this study we apply a genetic algorithm to a set of RNA sequences to find common RNA secondary structures. Our method is a three-step procedure. At the first stage of the procedure for each sequence, a genetic algorithm is used to optimize the structures in a population to a certain degree of stability. In this step, the free energy of a structure is the fitness criterion for the algorithm. Next, for each structure, we define a measure of structural conservation with respect to those in other sequences. We use this measure in a genetic algorithm to improve the structural similarity among sequences for the structures in the population of a sequence. Finally, we select those structures satisfying certain conditions of structural stability and similarity as predicted common structures for a set of RNA sequences. We have obtained satisfactory results from a set of tRNA, 5S rRNA, rev response elements (RRE) of HIV-1 and RRE of HIV-2/SIV, respectively.Keywords
This publication has 17 references indexed in Scilit:
- RAGA: RNA sequence alignment by genetic algorithmNucleic Acids Research, 1997
- Finding the most significant common sequence and structure motifs in a set of RNA sequencesNucleic Acids Research, 1997
- Alignment of possible secondary structures in multiple RNA sequences using simulated annealingBioinformatics, 1996
- Thermodynamic Prediction of Conserved Secondary Structure: Application to the RRE Element of HIV, the tRNA-like Element of CMV and the mRNA of Prion ProteinJournal of Molecular Biology, 1996
- An annealing mutation operator in the genetic algorithms for RNA foldingBioinformatics, 1996
- A genetic algorithm to search for optimal and suboptimal RNA secondary structuresBiophysical Chemistry, 1995
- ‘Well-determined’ regions in RNA secondary structure prediction: analysis of small subunit ribosomal RNANucleic Acids Research, 1995
- The Computer Simulation of RNA Folding Pathways Using a Genetic AlgorithmJournal of Molecular Biology, 1995
- RNA sequence analysis using covariance modelsNucleic Acids Research, 1994
- Common structures of the 5′ non-coding RNA in enteroviruses and rhinovirusesJournal of Molecular Biology, 1990