Real-time primer design for DNA chips

descriptionPublicationkeyboard_double_arrow_right Article , Conference object 22 Mar 2004Publisher:IEEE Comput. SocJournal:Proceedings International Parallel and Distributed Processing Symposium

Authors: Harald Simmler; Holger Singpiel; Reinhard Männer;

doi: 10.1109/ipdps.2003.1213288 , 10.1002/cpe.810

Real-time primer design for DNA chips

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Abstract

AbstractThe 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. Copyright © 2004 John Wiley & Sons, Ltd.

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University of Mannheim
Germany

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