Read Mapping Algorithms for Single Molecule Sequencing Data
WABI '08 Proceedings of the 8th international workshop on Algorithms in Bioinformatics
High performance protein sequence database scanning on the Cell Broadband Engine
Scientific Programming - High Performance Computing with the Cell Broadband Engine
The new SIMD Implementation of the Smith-Waterman Algorithm on Cell Microprocessor
Fundamenta Informaticae
CUDAlign: using GPU to accelerate the comparison of megabase genomic sequences
Proceedings of the 15th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming
SMC'09 Proceedings of the 2009 IEEE international conference on Systems, Man and Cybernetics
Acceleration of the Smith-Waterman algorithm using single and multiple graphics processors
Journal of Computational Physics
Protein similarity search with subset seeds on a dedicated reconfigurable hardware
PPAM'07 Proceedings of the 7th international conference on Parallel processing and applied mathematics
Parallelisation of sequence comparison algorithms using hybridised parallel techniques
HONET'09 Proceedings of the 6th international conference on High capacity optical networks and enabling technologies
Lock-free parallel dynamic programming
Journal of Parallel and Distributed Computing
Proceedings of the 19th ACM International Symposium on High Performance Distributed Computing
High performance technique for database applications using a hybrid GPU/CPU platform
Proceedings of the 21st edition of the great lakes symposium on Great lakes symposium on VLSI
HLS tools for FPGA: faster development with better performance
ARC'11 Proceedings of the 7th international conference on Reconfigurable computing: architectures, tools and applications
Parametrizing multicore architectures for multiple sequence alignment
Proceedings of the 8th ACM International Conference on Computing Frontiers
Parallel performance evaluation of multithreaded local sequence alignment
Proceedings of the 12th International Conference on Computer Systems and Technologies
CUDA-BLASTP: Accelerating BLASTP on CUDA-Enabled Graphics Hardware
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Fast and accurate similarity searching of biopolymer sequences with GPU and CUDA
ICA3PP'11 Proceedings of the 11th international conference on Algorithms and architectures for parallel processing - Volume Part I
Extending a C-like language for portable SIMD programming
Proceedings of the 17th ACM SIGPLAN symposium on Principles and Practice of Parallel Programming
Microprocessors & Microsystems
Characterization of Smith-Waterman sequence database search in X10
Proceedings of the 2012 ACM SIGPLAN X10 Workshop
High performance biological pairwise sequence alignment: FPGA versus GPU versus cell BE versus GPP
International Journal of Reconfigurable Computing - Special issue on High-Performance Reconfigurable Computing
Optimization schemes and performance evaluation of Smith–Waterman algorithm on CPU, GPU and FPGA
Concurrency and Computation: Practice & Experience
Performance comparison of GPU programming frameworks with the striped Smith-Waterman algorithm
ACM SIGARCH Computer Architecture News - ACM SIGARCH Computer Architecture News/HEART '12
Multi-parallel prefiltering on the convey HC-1 for supporting homology detection
Proceedings of the 20th European MPI Users' Group Meeting
IEEE Transactions on Very Large Scale Integration (VLSI) Systems
A Hardware Viewpoint on Biosequence Analysis: What’s Next?
ACM Journal on Emerging Technologies in Computing Systems (JETC) - Special Issue on Bioinformatics
Parallelizing dynamic programming through rank convergence
Proceedings of the 19th ACM SIGPLAN symposium on Principles and practice of parallel programming
Fine-grained parallel implementations for SWAMP+ Smith-Waterman alignment
Parallel Computing
| Hi-index | 3.84 |
Motivation: The only algorithm guaranteed to find the optimal local alignment is the Smith--Waterman. It is also one of the slowest due to the number of computations required for the search. To speed up the algorithm, Single-Instruction Multiple-Data (SIMD) instructions have been used to parallelize the algorithm at the instruction level. Results: A faster implementation of the Smith--Waterman algorithm is presented. This algorithm achieved 2--8 times performance improvement over other SIMD based Smith--Waterman implementations. On a 2.0 GHz Xeon Core 2 Duo processor, speeds of 3.0 billion cell updates/s were achieved. Availability: http://farrar.michael.googlepages.com/Smith-waterman Contact: farrar.michael@gmail.com