Result Details

Architecture Model for Approximate Tandem Repeat Detection

MARTÍNEK, T.; LEXA, M. Architecture Model for Approximate Tandem Repeat Detection. 22nd IEEE International Conference on Application-specific Systems, Architectures and Processors. Santa Monica, California: IEEE Computer Society, 2011. p. 239-242. ISBN: 978-1-4577-1290-6.
Type
conference paper
Language
English
Authors
Martínek Tomáš, doc. Ing., Ph.D., DCSY (FIT)
Lexa Matej, Ing., Ph.D., DCSY (FIT)
Abstract

Algorithms for biological sequence analysis, such as approximate string matching or algorithms for identification of sequence patterns supporting specific structural elements, present good opportunities for hardware acceleration. Implementation of these algorithms often results in architectures based on multidimensional arrays of computing elements. Mapping effectively these computational structures on FPGAs remains one of the challenging problems. This paper focuses on a specific hardware architecture for detection of approximate tandem repeats in sequences. We show how to create a parametrized architecture model combined with an automatic technique that can determine appropriate circuit dimensions with respect to input task parameters and the target platform properties.

Keywords

Approximate tandem repeat; Architecture model; Automated mapping; FPGA;

Published
2011
Pages
239–242
Proceedings
22nd IEEE International Conference on Application-specific Systems, Architectures and Processors
Conference
22nd IEEE International Conference on Application-specific Systems, Architectures and Processors
ISBN
978-1-4577-1290-6
Publisher
IEEE Computer Society
Place
Santa Monica, California
DOI
10.1109/ASAP.2011.6043277
BibTeX 
@inproceedings{BUT76394,
  author="Tomáš {Martínek} and Matej {Lexa}",
  title="Architecture Model for Approximate Tandem Repeat Detection",
  booktitle="22nd IEEE International Conference on Application-specific Systems, Architectures and Processors",
  year="2011",
  pages="239--242",
  publisher="IEEE Computer Society",
  address="Santa Monica, California",
  doi="10.1109/ASAP.2011.6043277",
  isbn="978-1-4577-1290-6",
  url="https://www.fit.vut.cz/research/publication/9671/"
}
Files
Projects
Advanced secured, reliable and adaptive IT, BUT, Vnitřní projekty VUT, FIT-S-11-1, start: 2011-01-01, end: 2013-12-31, completed
In vitro and in silico identification of non-canonical DNA structures in genomic sequences, GACR, Standardní projekty, GA204/08/1560, start: 2008-04-01, end: 2010-12-31, completed
Security-Oriented Research in Information Technology, MŠMT, Institucionální prostředky SR ČR (např. VZ, VC), MSM0021630528, start: 2007-01-01, end: 2013-12-31, running
Research groups
Reconfigurable Architecture Research Group (RG FPGA)
Departments
Department of Computer Systems (DCSY)
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