Publication details

Genomic PCR simulation with hardware-accelerated approximate sequence matching


LEXA Matej MARTÍNEK Tomáš BECK Patrik FUČÍK Otto VALLE Giorgio ZARA Ivano

Year of publication 2007
Type Article in Proceedings
Conference Proceedings 21st European Conference on Modelling and Simulation
MU Faculty or unit

Faculty of Informatics

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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