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Digital Library of the
European Council for Modelling and Simulation |
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Title: |
Genomic PCR Simulation With Hardware-Accelerated Approximate Sequence
Matching |
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Authors: |
Matej Lexa, Tomáš Martínek,
Patrik Beck, Otto Fučík,
Giorgio Valle, Ivano Zara |
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Published in:
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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 |
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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. |
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DOI: |
http://dx.doi.org/10.7148/2007-0333 |
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Abstract: |
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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