Search Results for "alignment"

The first parallel Smith-Waterman algorithm exploiting Intel Xeon Phi clusters to accelerate the alignment of long DNA sequences. This algorithm is written in C++ (with a set of SIMD intrinsic extensions), OpenMP and MPI. The performance evaluation revealed that our algorithm achieves very stable performance, and yields a performance of up to 30.1 GCUPS on a single Xeon Phi and up to 111.4 GCUPS on four Xeon Phis sharing a host.

...S-Match contains implementations of the semantic matching, minimal semantic matching and structure preserving semantic matching algorithms. S-Match applies as a solution in many fields, including: information integration, ontology evolution and alignment, peer-to-peer information sharing, digital libraries integration, web service composition, agent communication, and query answering on the web. S-Match is extendable to host new algorithms.

CUSHAW2 is a fast and parallel gapped read alignment to large genomes, such as the human genome. The performance evaluation, by aligning simulated and real datasets to the human genome, shows that CUSHAW2 is consistently among the highest-ranked aligners in terms of alignment quality for both single-end and paired-end alignment, while demonstrating highly competitive speed. Furthermore, our aligner shows good parallel scalability with respect to the number of CPU threads.

NeoBio is a Java class library of Computational Biology Algorithms. The current version consists mainly of pairwise sequence alignment algorithms such as the classical dynamic programming methods of Needleman-Wunsch and Smith-Waterman.