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LEXA, M. MARTÍNEK, T. BECK, P. FUČÍK, O. VALLE, G. ZARA, I.
Original Title
Genomic PCR simulation with hardware-accelerated approximate sequence matching
Type
conference paper
Language
English
Original 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.
Keywords
Virtual PCR; FPGA; sequence alignment; mathematical model
Authors
LEXA, M.; MARTÍNEK, T.; BECK, P.; FUČÍK, O.; VALLE, G.; ZARA, I.
RIV year
2007
Released
4. 6. 2007
Publisher
European Council for Modelling and Simulation
Location
Praha
ISBN
978-0-9553018-2-7
Book
21st European Conference on Modelling and Simulation
Pages from
333
Pages to
338
Pages count
6
BibTex
@inproceedings{BUT26056, author="Matej {Lexa} and Tomáš {Martínek} and Patrik {Beck} and Otto {Fučík} and Giorgio {Valle} and Ivano {Zara}", title="Genomic PCR simulation with hardware-accelerated approximate sequence matching", booktitle="21st European Conference on Modelling and Simulation", year="2007", pages="333--338", publisher="European Council for Modelling and Simulation", address="Praha", isbn="978-0-9553018-2-7" }