Heuristically Tuned GA to Solve Genome Fragment Assembly Problem

We proposed a genetic algorithm (GA) approach to solve the genome sequencing problem. The main contribution of this work is to add two ideas to improve the efficiency of the algorithm -(1) a chromosome reduction step (CRed) method to shorten the length of the chromosome and thereby the search-space, and (2) chromosome refinement step (CRef) is a greedy heuristics to locally improve the fitness of chromosomes. The algorithm will bring out longer and longer contigs with shorter and shorter gaps, as it continues running. At any stage the user can view the result, stop it when the output serves her/his purpose, or continue for getting longer contigs. We ran the proposed algorithm on part of the Wolbachia project work, and compared the results.

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