FPGASW: Accelerating Large-Scale Smith–Waterman Sequence Alignment Application with Backtracking on FPGA Linear Systolic Array

[1]  Che-Lun Hung,et al.  Accelerating Smith-Waterman Alignment for Protein Database Search Using Frequency Distance Filtration Scheme Based on CPU-GPU Collaborative System , 2015, International journal of genomics.

[2]  Aleksandar Stojmirovic,et al.  Log-odds sequence logos , 2015, Bioinform..

[3]  Chao Wang,et al.  Accelerating the Next Generation Long Read Mapping with the FPGA-Based System , 2014, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[4]  Yongchao Liu,et al.  CUDASW++ 3.0: accelerating Smith-Waterman protein database search by coupling CPU and GPU SIMD instructions , 2013, BMC Bioinformatics.

[5]  Paulo F. Flores,et al.  Integrated Hardware Architecture for Efficient Computation of the $n$-Best Bio-Sequence Local Alignments in Embedded Platforms , 2012, IEEE Transactions on Very Large Scale Integration (VLSI) Systems.

[6]  Carl Ebeling,et al.  Hardware Acceleration of Short Read Mapping , 2012, 2012 IEEE 20th International Symposium on Field-Programmable Custom Computing Machines.

[7]  Rainer G. Spallek,et al.  Short-Read Mapping by a Systolic Custom FPGA Computation , 2012, 2012 IEEE 20th International Symposium on Field-Programmable Custom Computing Machines.

[8]  Wen Tang,et al.  Accelerating Millions of Short Reads Mapping on a Heterogeneous Architecture with FPGA Accelerator , 2012, 2012 IEEE 20th International Symposium on Field-Programmable Custom Computing Machines.

[9]  Zaid Al-Ars,et al.  GPU-accelerated protein sequence alignment , 2011, 2011 Annual International Conference of the IEEE Engineering in Medicine and Biology Society.

[10]  Torbjørn Rognes,et al.  Faster Smith-Waterman database searches with inter-sequence SIMD parallelisation , 2011, BMC Bioinformatics.

[11]  Erik Vermij,et al.  Genetic sequence alignment on a supercomputing platform , 2011 .

[12]  Sanjay V. Rajopadhye,et al.  Improving CUDASW++, a Parallelization of Smith-Waterman for CUDA Enabled Devices , 2011, 2011 IEEE International Symposium on Parallel and Distributed Processing Workshops and Phd Forum.

[13]  Alexandros Stamatakis,et al.  Accelerating Phylogeny-Aware Short DNA Read Alignment with FPGAs , 2011, 2011 IEEE 19th Annual International Symposium on Field-Programmable Custom Computing Machines.

[14]  Yongchao Liu,et al.  CUDASW++2.0: enhanced Smith-Waterman protein database search on CUDA-enabled GPUs based on SIMT and virtualized SIMD abstractions , 2010, BMC Research Notes.

[15]  Massimo Torquati,et al.  Efficient Smith-Waterman on Multi-core with FastFlow , 2010, 2010 18th Euromicro Conference on Parallel, Distributed and Network-based Processing.

[16]  Yongchao Liu,et al.  MSA-CUDA: Multiple Sequence Alignment on Graphics Processing Units with CUDA , 2009, 2009 20th IEEE International Conference on Application-specific Systems, Architectures and Processors.

[17]  Witold R. Rudnicki,et al.  An efficient implementation of Smith Waterman algorithm on GPU using CUDA, for massively parallel scanning of sequence databases , 2009, 2009 IEEE International Symposium on Parallel & Distributed Processing.

[18]  Yongchao Liu,et al.  Parallel reconstruction of neighbor-joining trees for large multiple sequence alignments using CUDA , 2009, 2009 IEEE International Symposium on Parallel & Distributed Processing.

[19]  M. Schimmler,et al.  A Massively Parallel Architecture for Bioinformatics , 2009, ICCS.

[20]  Yongchao Liu,et al.  CUDASW++: optimizing Smith-Waterman sequence database searches for CUDA-enabled graphics processing units , 2009, BMC Research Notes.

[21]  Ying Liu,et al.  A Highly Parameterized and Efficient FPGA-Based Skeleton for Pairwise Biological Sequence Alignment , 2009, IEEE Transactions on Very Large Scale Integration (VLSI) Systems.

[22]  Sudarsan Padhy,et al.  A Reconfigurable Accelerator for Parallel Longest Common Protein Subsequence Algorithm , 2009, 2009 IEEE International Advance Computing Conference.

[23]  Cole Trapnell,et al.  Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.

[24]  Q. Snell,et al.  Sequence Alignment with Traceback on Reconfigurable Hardware , 2008, 2008 International Conference on Reconfigurable Computing and FPGAs.

[25]  Giorgio Valle,et al.  CUDA compatible GPU cards as efficient hardware accelerators for Smith-Waterman sequence alignment , 2008, BMC Bioinformatics.

[26]  Guang R. Gao,et al.  Implementation of the Smith-Waterman algorithm on a reconfigurable supercomputing platform , 2007, HPRCTA.

[27]  Martin C. Herbordt,et al.  Families of FPGA-based accelerators for approximate string matching , 2007, Microprocess. Microsystems.

[28]  Heitor Silvério Lopes,et al.  Implementation of a Parallel Algorithm for Protein Pairwise Alignment Using Reconfigurable Computing , 2006, 2006 IEEE International Conference on Reconfigurable Computing and FPGA's (ReConFig 2006).

[29]  Mustafa Gök,et al.  Efficient Cell Designs for Systolic Smith-Waterman Implementations , 2006, 2006 International Conference on Field Programmable Logic and Applications.

[30]  Aamer Jaleel,et al.  Last level cache (LLC) performance of data mining workloads on a CMP - a case study of parallel bioinformatics workloads , 2006, The Twelfth International Symposium on High-Performance Computer Architecture, 2006..

[31]  Bertil Schmidt,et al.  Hyper customized processors for bio-sequence database scanning on FPGAs , 2005, FPGA '05.

[32]  M. Herbordt,et al.  Families of FPGA-based algorithms for approximate string matching , 2004, Proceedings. 15th IEEE International Conference on Application-Specific Systems, Architectures and Processors, 2004..

[33]  Piotr Bala,et al.  Large Scale Protein Sequence Alignment Using FPGA Reprogrammable Logic Devices , 2004, FPL.

[34]  Vittorio Rosato,et al.  Designing hardware for protein sequence analysis , 2003, Bioinform..

[35]  Akihiko Konagaya,et al.  High Speed Homology Search with FPGAs , 2001, Pacific Symposium on Biocomputing.

[36]  J. Thompson,et al.  CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. , 1994, Nucleic acids research.

[37]  Dzung T. Hoang,et al.  Searching genetic databases on Splash 2 , 1993, [1993] Proceedings IEEE Workshop on FPGAs for Custom Computing Machines.

[38]  Barry S. Fagin,et al.  A special-purpose processor for gene sequence analysis , 1993, Comput. Appl. Biosci..

[39]  Dzung T. Hoang.  A Systolic Array for the Sequence Alignment Problem , 1992 .

[40]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[41]  M S Waterman,et al.  Identification of common molecular subsequences. , 1981, Journal of molecular biology.

[42]  Weikuan Yu,et al.  Performance Evaluation of FPGA-Based Biological Applications , 2007 .

[43]  Wang Dong,et al.  The Implementation and Analysis of Smith-Waterman Algorithm on Systolic Array , 2004 .

[44]  The BIOCCELERATOR for GCG users , 1994 .

[45]  Heng Li,et al.  BIOINFORMATICS ORIGINAL PAPER , 2022 .