A multi-threaded DNA tag/anti-tag library generator for multi-core platforms

Abstract

This paper describes a new approach to the problem of generating DNA tag/anti-tag libraries for use in biological assay methods. This approach couples multi-threaded coding methods and a highly parallel multi-population genetic algorithm to leverage performance gains made possible by the multi-core CPUs increasingly prevalent in today's commodity computers. We also describe the results of experiments characterizing the performance of this approach, which can yield up to an 8X speedup on a workstation equipped with dual quad-core CPUs. We observe that the coding effort required to implement this approach using the C language and Pthreads parallel programming model is greatly reduced compared to previous methods using both the VHDL language and reconfigurable hardware (FPGAs), and compared to C with the MPI API run on a cluster of computers.