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Architecture Model for Approximate Tandem Repeat Detection

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MARTÍNEK Tomáš LEXA Matej

Rok publikování 2011
Druh Článek ve sborníku
Konference 22nd IEEE International Conference on Application-specific Systems, Architectures and Processors
Fakulta / Pracoviště MU

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Citace
Doi http://dx.doi.org/10.1109/FCCM.2010.21
Obor Informatika
Klíčová slova Approximate tandem repeat; Architecture model; Automated mapping; FPGA;
Popis 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.
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