The design of PCR or DNA chip experiments is a time‐consuming process where bioinformatics is extensively used. The selection of the primers, which are immobilized on the DNA chip, requires a complex algorithm. Based on several parameters an optimized set of primers is automatically determined for a given gene sequence. This paper describes a parallel architecture which performs the optimization of the primer selection on a hardware accelerator. In contrast to the pure software approach, the parallel architecture gains a speedup of factor 500 using a PCI‐based hardware accelerator. This approach allows an optimization of a specified primer set in real time.
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Simmler et al. (2004) studied this question.
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