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Exploring I/O Strategies for Parallel Sequence-Search Tools with S3aSim

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Executive Summary

Parallel sequence-search tools are rising in popularity among computational biologists. With the rapid growth of sequence databases, database segmentation is the trend of the future for such search tools. While I/O currently is not a significant bottleneck for parallel sequence-search tools, future technologies including faster processors, customized computational hardware such as FPGAs, improved search algorithms, and exponentially growing databases will emphasize an increasing need for efficient parallel I/O in future parallel sequence-search tools. The authors' paper focuses on examining different I/O strategies for these future tools in a modern parallel file system (PVFS2).

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