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The RNA structural alignment is one of the most challenging tasks in bioinformatics. However, finding the accurate conserved structure of a set of RNA sequences is still being a difficult task. In this work, the problem is cast as an optimization problem for which a new framework relaying on hybrid genetic algorithm is proposed. The contribution consists in using a new objective function based on the Structure Conservation Index (SCI). In order to enhance the Genetic Algorithms (GA) performances, a Simulated Annealing (SA) procedure has been used. The proposed algorithm is composed on two phases.The first phase consists of applying a genetic algorithm.In the second phase, the simulated annealing procedure is applied in order to improve the final population given by the genetic algorithm. Experiments on a wide range of data sets have shown the effectiveness of the proposed framework and its ability to achieve good quality solutions comparing to those given by others techniques. General TermsAlgorithms,bioinformatic, metaheuristic, optimization problem.

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