Parallel Protein Information Analysis (PAPIA) System Running on a 64-Node PC Cluster

Yutaka Akiyama (
Kentaro Onizuka (
Tamotsu Noguchi (
Makoto Ando (

Parallel Application Laboratory, Real World Computing Partnership (RWCP)
Tsukuba Mitsui Bldg., 1-6-1 Takezono, Tsukuba 305-0032, Japan


Protein information analysis is widely regarded as a key technology in drug design, macromolecular engineering, and understanding genome sequences. Because vast amount of calculations are required, further speed-up for protein information analysis is very much in demand. We have implemented the PAPIA (PArallel Protein Information Analysis) system on the RWC PC cluster IIa ("PAPIA cluster") which consists of 64 Pentium Pro 200MHz microprocessors. The PAPIA system performs fast parallel processing for typical calculations in protein analysis, such as structure similarity search, sequence homology search and multiple sequence alignment, nearly 60 times faster than a single processor. We have started a WWW service (, allowing any biologist to easily submit jobs to the PAPIA system through a WWW browser. The user can experience the power of current parallel processing technology.

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Japanese Society for Bioinformatics