Digital Library

of the European Council for Modelling and Simulation



Genomic PCR Simulation With Hardware-Accelerated Approximate

Sequence Matching


Matej Lexa, Tomáš Martínek, Patrik Beck, Otto Fučík, Giorgio Valle,

Ivano Zara

Published in:


ECMS 2007 Proceedings

Edited by: Ivan Zelinka, Zuzana Oplatkova, Alessandra Orsoni


ISBN: 978-0-9553018-2-7

Doi: 10.7148/2007


21st European Conference on Modelling and Simulation,

Prague, June 4-6, 2007


Citation format:

Lexa, M., Martinek, T., Beck, P., Fucik, O., Valle, G., & Zara, I. (2007). Genomic PCR Simulation With Hardware-Accelerated Approximate Sequence Matching. ECMS 2007 Proceedings edited by: I. Zelinka, Z. Oplatkova, A. Orsoni (pp. 333-338). European Council for Modeling and Simulation. doi:10.7148/2007-0333.



We report the latest details on improvements made or planned for the VPCR simulation software currently accessible on the Internet (installed on servers in Padova and Brno). 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 PRIMEX similarity search program resulted in a marked improvement of PCR product predictions. Further speed improvements were acheived using hardware acceleration of approximate sequence matching. We report our theorethical compu- tation time estimates and results of the first tests using the Arabidopis and human genome sequences as PCR templates.

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