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ScalaBLAST 2.0: rapid and robust BLAST calculations on multiprocessor systems
Christopher S Oehmen1, Douglas J Baxter
1Pacific Northwest National Laboratory, Richland, WA 99352, USA. christopher.oehmen@pnl.gov
Bioinformatics (Oxford, England)
|January 31, 2013
Summary
ScalaBLAST offers a parallel approach to Basic Local Alignment Search Tool (BLAST) calculations, leveraging over 16,000 processing cores. This robust, fault-resilient design provides extreme parallelism with minimal overhead compared to serial BLAST.
Area of Science:
- Computational Biology
- Bioinformatics
- Genomics
Background:
- Basic Local Alignment Search Tool (BLAST) is a cornerstone of computational biology.
- Exponential growth in sequence data necessitates scalable analysis tools.
- Increased accessibility of multicore systems and clusters enables parallel processing.
Purpose of the Study:
- To develop a parallelized version of BLAST for enhanced computational efficiency.
- To design a robust and fault-resilient system for large-scale sequence analysis.
- To minimize overhead and maintain performance compared to serial BLAST.
Main Methods:
- Implementation of ScalaBLAST on conventional multiprocessor systems.
- Exploitation of extreme parallelism using over 16,000 processing cores.
- Focus on a portable and fault-resilient design architecture.
Main Results:
- Demonstration of parallel BLAST calculations on a massive scale.
- Achieved high performance with minimal overhead relative to serial BLAST.
- Validated the robustness and fault-resilience of the ScalaBLAST design.
Conclusions:
- ScalaBLAST effectively addresses the computational demands of rapidly growing biological sequence data.
- The parallel architecture enables efficient, large-scale sequence alignment.
- ScalaBLAST provides a scalable and reliable solution for modern bioinformatics.
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