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Real‐time primer design for DNA chips
Author(s) -
Simmler H.,
Singpiel H.,
Männer R.
Publication year - 2004
Publication title -
concurrency and computation: practice and experience
Language(s) - English
Resource type - Book series
SCImago Journal Rank - 0.309
H-Index - 67
eISSN - 1532-0634
pISSN - 1532-0626
ISBN - 0-7695-1926-1
DOI - 10.1002/cpe.810
Subject(s) - primer (cosmetics) , speedup , computer science , set (abstract data type) , selection (genetic algorithm) , chip , process (computing) , software , parallel computing , instruction set , embedded system , operating system , chemistry , programming language , artificial intelligence , telecommunications , organic chemistry
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. Copyright © 2004 John Wiley & Sons, Ltd.