Bioinformatics Performance Comparison of Many-core Tile64 vs. Multi-core Intel Xeon

The performance of the many-core Tile64 versus the multi-core Xeon x86 architecture on bioinformatics has been compared. We have used the pairwise algorithm MC64-NW/SW that we have previously developed to align nucleic acid (DNA and RNA) and peptide (protein) sequences for the benchmarking, being an enhanced and parallel implementation of the Needleman-Wunsch and Smith-Waterman algorithms. We have ported the MC64-NW/SW (originally developed for the Tile64 processor), to the x86 architecture (Intel Xeon Quad Core and Intel i7 Quad Core processors) with excellent results. Hence, the evolution of the x86-based architectures towards coprocessors like the Xeon Phi should represent significant performance improvements for bioinformatics.