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KMID : 0811720040080000186
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Korean Journal of Physiology & Pharmacology
2004 Volume.8 No. 0 p.186 ~ p.0
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Multiple Sequence Alignment and Efficient Data Management using Ultra Fast and High-performance Bioinformatics System
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Joo Hyun
Kim Tae-Ho
Kim Na-Ri
Youm Jae-Boum
Kim Eui-Yong
Han Jin
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Abstract
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Modern cutting-edge bioinformatics techniques have revolutionized the field of biomedical and e-health applications. We setup Linux-based parallel computing system using a message-passing interface (MPI) and OpenMosix to solve complex biological problems. The machine was applied for implementing high performance ClustalW-MPI which aligns massive protein or nucleotide sequences (including SNP Analysis). The system consists of twelve PC-based (Pentium4 1.8 GHz×4, AMD Athlon 2200+Dual×8) distributed memory processing modules integrated with high band-width networks (Intel Standalone). OpenMosix used in this system supports a preemptive process migration for dynamic CPU load-balancing, efficient kernel I/O, and memory ushering. To reduce space and time complexities of pair-align dynamic searching for each Smith-Waterman matrices loaded on computation nodes, MPI and OpenMosix load balancing algorithms were combined to migrate processes from over-loaded to less-loaded computation nodes. Based on this system, we also installed ClustalW-MPI Web version to provide Graphics User Interface (GUI).
Source: Korean Journal of Physiology & Pharmacology.2004 Oct;8(Suppl I):S138-S138
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KEYWORD
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Bioinformatics, Multiple Sequence Alignment, ClustalW-MPI, Cluster Computing, Biomedical
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