Abstract: Genomic sequence comparison algorithms represent the basic toolbox for processing large volume of DNA or protein sequences. They are involved both in the systematic scan of databases, mostly for detecting similarities with an unknown sequence, and in preliminary processing before advanced bioinformatics analysis. Due to the exponential growth of genomic data, new solutions are required to keep the computation time reasonable. This paper presents a specific hardware architecture to speed-up seed-based algorithms which are currently the most popular heuristics for detecting alignments. The architecture regroups FLASH and FPGA technologies on a common support, allowing a large amount of data to be rapidly accessed and quickly processed. Experiments on database search and intensive sequence comparison demonstrate a good cost/performance ratio compared to standard approaches.