Real-time primer design for DNA chips
| Autor: | Holger Singpiel, H. Simmler, Reinhard Männer |
|---|---|
| Rok vydání: | 2004 |
| Předmět: |
Speedup
Computer Networks and Communications business.industry Computer science Process (computing) Parallel computing Computer Science Applications Theoretical Computer Science law.invention Set (abstract data type) chemistry.chemical_compound Software Computational Theory and Mathematics chemistry law Hardware acceleration DNA microarray Primer (molecular biology) Field-programmable gate array business DNA Computer hardware Selection (genetic algorithm) Polymerase chain reaction |
| Zdroj: | IPDPS |
| DOI: | 10.1109/ipdps.2003.1213288 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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