Detail publikačního výsledku

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

Paper in proceedings outside WoS and Scopus

Original Abstract

We report the latest details on improvements made or planned for theVPCR simulation software currently accessible on the Internet. Wedescribe the inner workings of the dynamic amplification simulationmodel, concentrating mostly on the time- and sensitivity-critical stepof sequence matching. Replacement of BLAST by the more sensitive andfaster PRIMEX similarity search program resulted in a marked improvementof PCR product predictions. Further speed improvements were acheivedusing hardware acceleration of approximate sequence matching.

English abstract

We report the latest details on improvements made or planned for theVPCR simulation software currently accessible on the Internet. Wedescribe the inner workings of the dynamic amplification simulationmodel, concentrating mostly on the time- and sensitivity-critical stepof sequence matching. Replacement of BLAST by the more sensitive andfaster PRIMEX similarity search program resulted in a marked improvementof PCR product predictions. Further speed improvements were acheivedusing hardware acceleration of approximate sequence matching.

Keywords

Virtual PCR; FPGA; sequence alignment; mathematical model

Key words in English

Virtual PCR; FPGA; sequence alignment; mathematical model

Authors

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

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

Full text in the Digital Library

http://hdl.handle.net/

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"
}