Publication detail

Genomic PCR simulation with hardware-accelerated approximate sequence matching

LEXA, M. MARTÍNEK, T. BECK, P. FUČÍK, O. VALLE, G. ZARA, I.

Original Title

Genomic PCR simulation with hardware-accelerated approximate sequence matching

English Title

Genomic PCR simulation with hardware-accelerated approximate sequence matching

Type

conference paper

Language

en

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.

English 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

RIV year

2007

Released

04.06.2007

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

Documents

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",
  annote="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.",
  address="European Council for Modelling and Simulation",
  booktitle="21st European Conference on Modelling and Simulation",
  chapter="26056",
  howpublished="print",
  institution="European Council for Modelling and Simulation",
  year="2007",
  month="june",
  pages="333--338",
  publisher="European Council for Modelling and Simulation",
  type="conference paper"
}