Conference paper

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.
Publication language:english
Original title:Genomic PCR simulation with hardware-accelerated approximate sequence matching
Title (cs):Genomická PCR simulace s hardwarovou akcelerací operace hledani podobnosti
Pages:333-338
Proceedings:21st European Conference on Modelling and Simulation
Conference:21st European Conference on Modelling and Simulation
Place:Praha, CZ
Year:2007
ISBN:978-0-9553018-2-7
Publisher:European Council for Modelling and Simulation
Keywords
Virtual PCR; FPGA; sequence alignment; mathematical model
Annotation
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.
BibTeX:
@INPROCEEDINGS{
   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 = {http://www.fit.vutbr.cz/research/view_pub.php?id=8396}
}

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