Parallel genomic sequence-search on a massively parallel system

In the life sciences, genomic databases for sequence search have been growing exponentially in size. As a result, faster sequencesearch algorithms to search these databases continue to evolve to cope with algorithmic time complexity. The ubiquitous tool for such search is the Basic Local Alignment Search Tool (BLAST) [1] from the National Center for Biotechnology Information (NCBI). Despite continued algorithmic improvements in BLAST, it cannot keep up with the rate at which the database is exponentially increasing in size. Therefore, parallel implementations such as mpiBLAST have emerged to address this problem. The performance of such implementations depends on a myriad of factors including algorithmic, architectural, and mapping of the algorithm to the architecture. This paper describes modifications and extensions to a parallel and distributed-memory version of BLAST called mpiBLAST-PIO and how it maps to a massively parallel system, specifically IBM Blue Gene/L (BG/L). The extens...

• Type: Conference
• Year: 2007
• Where: CF
• Authors: Oystein Thorsen, Brian E. Smith, Carlos P. Sosa, Karl Jiang, Heshan Lin, Amanda E. Peters, Wu-chun Feng
• Keywords: Applied Computing, Basic Local Alignment Search Tool, Blue Gene/L, CF 2007, Massively Parallel