MC64-ClustalWP2: a highly-parallel hybrid strategy to align multiple sequences in many-core architectures.

ABSTRACT: We have developed the MC64-ClustalWP2 as a new implementation of the Clustal W algorithm, integrating a novel parallelization strategy and significantly increasing the performance when aligning long sequences in architectures with many cores. It must be stressed that in such a process, the detailed analysis of both the software and hardware features and peculiarities is of paramount importance to reveal key points to exploit and optimize the full potential of parallelism in many-core CPU systems. The new parallelization approach has focused into the most time-consuming stages of this algorithm. In particular, the so-called progressive alignment has drastically improved the performance, due to a fine-grained approach where the forward and backward loops were unrolled and parallelized. Anoth

SUBMITTER: Diaz D 

PROVIDER: S-EPMC3977933 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature