Detail publikace

Architecture Model for Approximate Tandem Repeat Detection

Originální název

Architecture Model for Approximate Tandem Repeat Detection

Anglický název

Architecture Model for Approximate Tandem Repeat Detection

Jazyk

en

Originální abstrakt

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.

Anglický abstrakt

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.

BibTex


@inproceedings{BUT76394,
  author="Tomáš {Martínek} and Matej {Lexa}",
  title="Architecture Model for Approximate Tandem Repeat Detection",
  annote="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.",
  address="IEEE Computer Society",
  booktitle="22nd IEEE International Conference on Application-specific Systems, Architectures and Processors",
  chapter="76394",
  doi="10.1109/ASAP.2011.6043277",
  edition="NEUVEDEN",
  howpublished="online",
  institution="IEEE Computer Society",
  year="2011",
  month="june",
  pages="239--242",
  publisher="IEEE Computer Society",
  type="conference paper"
}