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Reconfigurable systems for sequence alignment and for general dynamic programming.

Ricardo P Jacobi1, Mauricio Ayala-Rincón, Luis G A Carvalho

  • 1Departamento de Ciência da Computação, Universidade de Brasília, Brasília, DF, Brazil. rjacobi@cic.unb.br

Genetics and Molecular Research : GMR
|December 13, 2005
PubMed
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This summary is machine-generated.

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This study introduces a novel reconfigurable systolic architecture for dynamic programming. This hardware acceleration offers significant speedups for sequence alignment and string matching tasks.

Area of Science:

  • Computer Science
  • Bioinformatics
  • Hardware Architecture

Background:

  • Systolic arrays offer inherent parallelism for computational problems.
  • Dynamic programming algorithms are crucial for bioinformatics tasks like sequence alignment.
  • Existing software solutions can be computationally intensive.

Purpose of the Study:

  • To present a novel reconfigurable systolic architecture.
  • To demonstrate its application in dynamic programming for bioinformatics.
  • To evaluate its performance against software alternatives.

Main Methods:

  • Developed a reconfigurable systolic architecture.
  • Applied the architecture to dynamic programming problems including sequence alignment.
  • Implemented the architecture using VHDL on an APEX FPGA.

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Main Results:

  • The architecture efficiently handles dynamic programming methods.
  • Dynamicity of reconfigurability proved beneficial for sequence alignment construction.
  • Achieved several magnitudes faster performance compared to software algorithms.

Conclusions:

  • Reconfigurable systolic arrays provide efficient solutions for complex computational problems.
  • The proposed architecture offers significant performance gains for bioinformatics applications.
  • FPGA implementation demonstrates practical feasibility and speed advantages.