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.
Heuristic
cuBLASTP
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.
muBLASTP
Optimized for , ,
An accelerated, database-indexed BLAST algorithm for protein sequence search on multicore CPUs.
mpiBLAST
Optimized for , , , 
A freely available, open-source, parallel implementation of NCBI BLAST, which scales from laptops and desktops to servers and supercomputer.
centroidBLAST
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.
Smith-Waterman
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.
Needleman-Wunsch
Optimized for GPU-enabled , ,
A GPU-accelerated approach to optimal global alignment for NVIDIA GPUs.
AAlign
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.
