Publication Details

Architecture Model for Approximate Tandem Repeat Detection

MARTÍNEK Tomáš and LEXA Matej. Architecture Model for Approximate Tandem Repeat Detection. In: 22nd IEEE International Conference on Application-specific Systems, Architectures and Processors. Santa Monica, California: IEEE Computer Society, 2011, pp. 239-242. ISBN 978-1-4577-1290-6.
Czech title
Model architektury pro hledání přibližných tandemových opakování
Type
conference paper
Language
english
Authors
Martínek Tomáš, doc. Ing., Ph.D. (DCSY FIT BUT)
Lexa Matej, Ing., Ph.D. (FI MUNI)
Keywords

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

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.

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, Santa Monica, California, US
ISBN
978-1-4577-1290-6
Publisher
IEEE Computer Society
Place
Santa Monica, California, US
DOI
10.1109/ASAP.2011.6043277
BibTeX 
@INPROCEEDINGS{FITPUB9671,
   author = "Tom\'{a}\v{s} Mart\'{i}nek and Matej Lexa",
   title = "Architecture Model for Approximate Tandem Repeat Detection",
   pages = "239--242",
   booktitle = "22nd IEEE International Conference on Application-specific Systems, Architectures and Processors",
   year = 2011,
   location = "Santa Monica, California, US",
   publisher = "IEEE Computer Society",
   ISBN = "978-1-4577-1290-6",
   doi = "10.1109/ASAP.2011.6043277",
   language = "english",
   url = "https://www.fit.vut.cz/research/publication/9671"
}
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