Cooperative and out-of-core execution of the irregular wavefront propagation pattern on hybrid machines with Intel Xeon Phi™.

The Irregular Wavefront Propagation Pattern (IWPP) is a core computing structure in several image analysis operations. Efficient implementation of IWPP on the Intel Xeon Phi is difficult because of the irregular data access and computation characteristics. The traditional IWPP algorithm relies on atomic instructions, which are not available in the SIMD set of the Intel Phi.

Foldalign 2.5: multithreaded implementation for pairwise structural RNA alignment.

Motivation: Structured RNAs can be hard to search for as they often are not well conserved in their primary structure and are local in their genomic or transcriptomic context. Thus, the need for tools which in particular can make local structural alignments of RNAs is only increasing.

Results: To meet the demand for both large-scale screens and hands on analysis through web servers, we present a new multithreaded version of Foldalign.