Iterated Local Search for de Novo Genomic Sequencing

in Lecture Notes in Computer Science (2010), 6114

The sequencing process of a DNA chain for reading its components supposes a complex process, since only small DNA fragments can be read nowadays. Therefore, the use of optimization algorithms is required ... [more ▼]

The sequencing process of a DNA chain for reading its components supposes a complex process, since only small DNA fragments can be read nowadays. Therefore, the use of optimization algorithms is required to rebuild a single chain from all the small pieces. We address here a simplified version of the problem, in which no errors in the sequencing process are allowed. The methods typically used in the literature for this problem are not satisfactory when solving realistic size instances, so there is a need for new more efficient and accurate methods. We propose a new iterated local search algorithm, highly competitive with the best algorithms in the literature, and considerably faster. [less ▲]

Evaluation of Different Optimization Techniques in the Design of Ad Hoc Injection Networks

in special session on Parallel and Grid Computing for Optimization as part of The 2008 International Conference High Performance Computing & Simulation (HPCS008) and in conjunction with The 22nd European Conference on Modeling and Simulation (ECMS 2008). (2008)

Optimal Design of Ad Hoc Injection Networks by Using Genetic Algorithms

in 9th annual conference on Genetic and evolutionary computation (GECCO '07) (2007)