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In this paper we present new approaches to high performance protein database scanning on two novel massively parallel architectures to gain supercomputer power at low cost. The first architecture is built around a Beowulf PC-cluster linked by a high-speed network and fine-grained parallel Systola 1024 processor boards connected to each node. The second architecture is the Fuzion 150, a new parallel computer with a linear SIMD array of 1536 processing elements on a single chip. We present the design of a database scanning application based on the Smith-Waterman algorithm in order to derive efficient mappings onto these architectures. The implementations lead to significant runtime savings for large-scale database scanning. This result shows that both architectures provide high-throughput sequence similarity analysis solutions at a good price/performance ratio.