Genomic PCR simulation with hardware-accelerated approximate sequence matching
| Authors | |
|---|---|
| Year of publication | 2007 |
| Type | Article in Proceedings |
| Conference | Proceedings 21st European Conference on Modelling and Simulation |
| MU Faculty or unit | |
| Citation | |
| Field | Computer hardware and software |
| Keywords | Virtual PCR; FPGA; sequence alignment; mathematical model |
| Description | We report the latest details on improvements made or planned for the VPCR simulation software currently accessible on the Internet. We describe the inner workings of the dynamic amplification simulation model, concentrating mostly on the time- and sensitivity-critical step of sequence matching. Replacement of BLAST by the more sensitive and faster PRMEX similarity search program resulted in a marked improvement of PCR product predictions. Further speed improvements were acheived using hardware acceleration of approximate sequence matching. |
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