Hybrid Cuckoo Search for solving DNA Fragment Assembly Problem

ROJAS MATÍAS GABRIEL; PABLO JAVIER VIDAL; JESSICA ANDREA CARBALLIDO; ANA CAROLINA OLIVERA

Mendoza

Congreso; IV Congreso Internacional de Ciencias de la Computación y Sistemas de Información; 2020

Universidad Champagnat

The Deoxyribonucleic Acid Fragment Assembly Problem represents an interesting research topic in the field of bioinformatics. This problem consists in reconstructing a DNA chain as close to the original sequence from a set of DNA fragments taken randomly. Several authors have proposed different approaches to solve Deoxyribonucleic Acid Fragment Assembly Problem. In particular, nature-inspired algorithms has been used for its resolution. Among these techniques, the Cuckoo Search is a recent method based on the breeding of the cuckoo birds. In this paper, a discrete Cuckoo Search algorithm is adapted to DNA-FAP hybridising with the behaviour of two different local searches to improve the search capabilities of the canonical algorithm. A numerical evaluation of both proposals and the canonical version is carried out using a well-known benchmark dataset. Results demonstrate that the hybridisation improves the search and transform the cuckoo search in a robust procedure with the potential to deal with longer sequences or sequences of unknown length as well.