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Reconfigurable Systems for Sequence Alignment and for General Dynamic Programming

9 years 11 months ago
Reconfigurable Systems for Sequence Alignment and for General Dynamic Programming
ABSTRACT. Reconfigurable systolic arrays can be adapted to efficiently resolve a wide spectrum of computational problems; parallelism is naturally explored in systolic arrays and reconfigurability allows for redefinition of the interconnections and operations even during run time (dynamically). We present a reconfigurable systolic architecture that can be applied for the efficient treatment of several dynamic programming methods for resolving well-known problems, such as global and local sequence alignment, approximate string matching and longest common subsequence. The dynamicity of the reconfigurability was found to be useful for practical applications in the construction of sequence alignments. A VHDL (VHSIC hardware description language) version of this new architecture was implemented on an APEX FPGA (Field programmable gate array). It would be several magnitudes faster than the software algorithm alternatives. Key words: Sequence alignment, Dynamic programming, Hardware, Reconfig...
Ricardo P. Jacobi, Mauricio Ayala-Rincón, L
Added 31 Oct 2010
Updated 31 Oct 2010
Type Conference
Year 2004
Where WOB
Authors Ricardo P. Jacobi, Mauricio Ayala-Rincón, Luis G. A. Carvalho, Carlos H. Llanos, Reiner W. Hartenstein
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