A FPGA-based hardware implementation of generalized profile search using online arithmetic

This paper describes the hardware implementation of the Generalized Profile Search algorithm using online arithmetic and redundant, data representation. This is part of the GenStorm project, aimed at providing a dedicated computer for biological sequence processing based on reconfigurable hardware using FPGAs. The serial evaluation of the result made possible by a redundant data representa.tion leads to a significant increase of data throughput in comparison with standard non redundant data coding.

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