Abstract

VIDAL, Pablo Javier  and  OLIVERA, Ana Carolina. DNA fragment assembling using a novel GPU firefly algorithm. Dyna rev.fac.nac.minas [online]. 2018, vol.85, n.204, pp.108-116. ISSN 0012-7353.  https://doi.org/10.15446/dyna.v85n204.60078.

The Deoxyribonucleic Acid Fragment Assembly Problem (DNA-FAP) consists in reconstruct a DNA chain from a set of fragments taken randomly. Several authors solved the DNA-FAP using different approaches. In general, although it was obtaining good results; the computational time associated is high. The Firefly Algorithm (FA) is a bioinspired model based on the behaviour of fireflies. Considering that FA is a population bioinspired algorithm is possible design a parallel model of itself on Graphics Processing. In this work, a FA especially development for its execution on GPU is presented in order to accelerate the computational process to solve the DNA-FAP. Through several experiments the efficiency of the algorithm and the quality of the results were demonstrated.

Keywords : fragment assembly problem; firefly algorithm; graphics processing units; optimization; parallelism.

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