Sequence Search

Sequence search is a method of searching similarities between a query sequence and sequences in database by using alignment. Similarities between the query sequence and a sequence of known function from the sequence database can help identify the function of the query sequence and potentially how to regulate it.


Optimized for GPU-enabled , ,

A GPU-accelerated and re-factored BLAST algorithm for protein sequence search on NVIDIA GPUs that delivers an additional 1.9-fold speedup over the fastest existing GPU-implemented BLAST.

Optimized for , ,

An accelerated, database-indexed BLAST algorithm for protein sequence search on multicore CPUs.

Optimized for , , ,

A freely available, open-source, parallel implementation of NCBI BLAST, which scales from laptops and desktops to servers and supercomputer.

Optimized for , ,

A scripting-based approach to BLAST that significantly accelerates performance by only searching on a representative fraction, i.e., centroid, of the original database.


Optimized for and GPU-enabled , ,

An innovative parallelization of optimal local alignment for the hybrid multicore architecture of the Sony Playstation 3 (PS3) and the IBM BladeCenter Q22.

Optimized for GPU-enabled , ,

A GPU-accelerated approach to optimal global alignment for NVIDIA GPUs.

Optimized for , ,

A framework for the automatic vectorization of pairwise seqeunce alignment, e.g., Smith-Waterman and Needleman-Wunsch, for x86-based systems, like Intel Haswell or Intel Knights Corner.

Download Paper to appear at IEEE IPDPS May 2016

Our research has been supported by:

Affiliated Sites: Virginia Tech · SEEC · Synergy

Last updated: January 2016