Publication Details

Genomic PCR simulation with hardware-accelerated approximate sequence matching

LEXA Matej, MARTÍNEK Tomáš, BECK Patrik, FUČÍK Otto, VALLE Giorgio and ZARA Ivano. Genomic PCR simulation with hardware-accelerated approximate sequence matching. In: 21st European Conference on Modelling and Simulation. Praha: European Council for Modelling and Simulation, 2007, pp. 333-338. ISBN 978-0-9553018-2-7.
Czech title
Genomická PCR simulace s hardwarovou akcelerací operace hledani podobnosti
Type
conference paper
Language
english
Authors
Lexa Matej, Ing., Ph.D. (FI MUNI)
Martínek Tomáš, doc. Ing., Ph.D. (DCSY FIT BUT)
Beck Patrik, Bc. (FIT BUT)
Fučík Otto, doc. Dr. Ing. (DCSY FIT BUT)
Valle Giorgio (UNIPD)
Zara Ivano (UNIPD)
Keywords

Virtual PCR; FPGA; sequence alignment; mathematical model

Abstract

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 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.

Published
2007
Pages
333-338
Proceedings
21st European Conference on Modelling and Simulation
Conference
21st European Conference on Modelling and Simulation, Praha, CZ
ISBN
978-0-9553018-2-7
Publisher
European Council for Modelling and Simulation
Place
Praha, CZ
BibTeX 
@INPROCEEDINGS{FITPUB8396,
   author = "Matej Lexa and Tom\'{a}\v{s} Mart\'{i}nek and Patrik Beck and Otto Fu\v{c}\'{i}k and Giorgio Valle and Ivano Zara",
   title = "Genomic PCR simulation with hardware-accelerated approximate sequence matching",
   pages = "333--338",
   booktitle = "21st European Conference on Modelling and Simulation",
   year = 2007,
   location = "Praha, CZ",
   publisher = "European Council for Modelling and Simulation",
   ISBN = "978-0-9553018-2-7",
   language = "english",
   url = "https://www.fit.vut.cz/research/publication/8396"
}
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