Title :
Real-time primer design for DNA chips
Author :
Simmler, H. ; Singpiel, H. ; Männer, R.
Author_Institution :
Acconovis GmbH, Mannheim, Germany
Abstract :
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 detected 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.
Keywords :
DNA; arrays; biology computing; optimisation; parallel architectures; real-time systems; DNA chips; PCI based hardware accelerator; PCR; bioinformatics; complex algorithm; gene sequence; optimization; optimized set; parallel architecture; polymerase chain reaction; real-time primer design; speedup; Bioinformatics; Biological cells; DNA; Databases; Genomics; Hardware; Parallel architectures; Polymers; Protocols; Sequences;
Conference_Titel :
Parallel and Distributed Processing Symposium, 2003. Proceedings. International
Print_ISBN :
0-7695-1926-1
DOI :
10.1109/IPDPS.2003.1213288