Architecture model for approximate tandem repeat detection

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 base...

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Bibliographic Details
Main Authors: Martinek, T., Lexa, M.
Format: Conference Proceeding
Language:English
Subjects:
Approximate tandem repeat
Architecture model
Automated mapping
Bandwidth
Computer architecture
Equations
Field programmable gate arrays
FPGA
Hardware
Integrated circuit modeling
Mathematical model
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Description
Summary: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.
ISSN:1063-6862
DOI:10.1109/ASAP.2011.6043277