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Direct approaches to exploit many-core architecture in bioinformatics

2012; Elsevier BV; Volume: 29; Issue: 1 Linguagem: Inglês

10.1016/j.future.2012.03.018

1872-7115

Francisco J. Esteban, David Díaz, Pilar Hernández, Juan Antonio Caballero, Gabriel Dorado, Sergio Gálvez,

RNA modifications and cancer

Current trends in computer programming look for solutions in the challenging task of porting and optimizing existing algorithms to many-core architectures with tens of Central Processing Units (CPUs). Yet, the lack of standardized general-purpose parallel programming and porting methodologies represents the main bottleneck on these developments. We have focused on bioinformatics applied to genomics in general and the so-called Next-Generation Sequencing (NGS) in particular, in order to study the viability and cost of porting and optimizing well known algorithms to a many-core architecture. Three different methods are tackled in order to implement existing algorithms in Tile64, corresponding to a microprocessor containing 64 CPUs, each of them being capable of executing an independent Linux operating system. Three different approaches have been explored: (i) implementation of the Needleman-Wunsch/Smith-Waterman pairwise aligner from scratch; (ii) direct translation of the Message Passing Interface (MPI) C++ ABySS assembly algorithm with changes on the communication layer; and (iii) migration of the ClustalW tool, parallelizing only the most time-consuming stage. The performance-gain/development-cost tradeoffs indicate that the Tile64 microprocessor has the potential to increase the performance of bioinformatics in an unprecedented way for a standalone Personal Computer (PC). Yet, the effective exploitation of these parallel implementations requires a detailed understanding of the peculiar many-core characteristics when migrating previous non-parallel source codes. Highlights? Computing power of the Tile64 many-core microprocessor can be exploited for NGS bioinformatics tasks. ? Tile64 many-core CPU architecture works as a cluster of pico-computers, as with the MC64-NW/SW algorithm. ? MC64-ClustalW shows an important performance improvement with a minor development effort. ? MC64-ABySS reveals that a MPI-like efficient API for Tile64 is essential to port successfully most of the existing parallel code. ? Wide-spreading of many-core CPU technologies could lead to a new paradigm in programming methodologies in the next years.