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2002
IEEE

Massively Parallel Solutions for Molecular Sequence Analysis

11 years 4 months ago
Massively Parallel Solutions for Molecular Sequence Analysis
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 PCcluster 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 SmithWaterman 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 highthroughput sequence similarity analysis solutions at a good price/performance ratio.
Bertil Schmidt, Heiko Schröder, Manfred Schim
Added 15 Jul 2010
Updated 15 Jul 2010
Type Conference
Year 2002
Where IPPS
Authors Bertil Schmidt, Heiko Schröder, Manfred Schimmler
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