Implementation of a programmable array processor architecture for approximate string matching algorithms on FPGAs

Authors:
Panagiotis D. Michailidis;Konstantinos G. Margaritis
Affiliations:
Parallel and Distributed Processing Laboratory, University of Macedonia, Department of Applied Informatics, Thessaloniki, Greece;Parallel and Distributed Processing Laboratory, University of Macedonia, Department of Applied Informatics, Thessaloniki, Greece
Venue:
IPDPS'06 Proceedings of the 20th international conference on Parallel and distributed processing
Year:
2006

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Abstract

Approximate string matching problem is a common and often repeated task in information retrieval and bioinformatics. This paper proposes a generic design of a programmable array processor architecture for a wide variety of approximate string matching algorithms to gain high performance at low cost. Further, we describe the architecture of the array and the architecture of the cell in detail in order to efficiently implement for both the preprocessing and searching phases of most string matching algorithms. Further, the architecture performs approximate string matching for complex patterns that contain don't care, complement and classes symbols. We also implement and evaluate the proposed architecture on a field programmable gate array (FPGA) device using the JHDL tool for synthesis and the Xilinx Foundation tools for mapping, placement, and routing. Finally, our programmable implementation achieves about 9-340 times faster than a desktop computer with a Pentium 4 3.5 GHz for all algorithms when the length of the pattern is 1024.