Accelerating DNA pairwise sequence alignment using FPGA and a customized convolutional neural network

[1]  Endri Bezati,et al.  Design space exploration of dataflow-based Smith-Waterman FPGA implementations , 2017, 2017 IEEE International Workshop on Signal Processing Systems (SiPS).

[2]  Armando De Giusti,et al.  SWIMM 2.0: Enhanced Smith–Waterman on Intel’s Multicore and Manycore Architectures Based on AVX-512 Vector Extensions , 2018, International Journal of Parallel Programming.

[3]  W. Pearson.  Comparison of methods for searching protein sequence databases , 1995, Protein science : a publication of the Protein Society.

[4]  David Donofrio,et al.  A Parallel, Energy Efficient Hardware Architecture for the merAligner on FPGA Using Chisel HCL , 2018, 2018 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW).

[5]  Quinn Snell,et al.  Hardware Accelerated Sequence Alignment with Traceback , 2009, Int. J. Reconfigurable Comput..

[6]  T. Ramdas,et al.  A Survey of FPGAs for Acceleration of High Performance Computing and their Application to Computational Molecular Biology , 2005, TENCON 2005 - 2005 IEEE Region 10 Conference.

[7]  Ying Liu,et al.  High Performance Biological Pairwise Sequence Alignment: FPGA versus GPU versus Cell BE versus GPP , 2012, Int. J. Reconfigurable Comput..

[8]  Nae-Chyun Chen,et al.  Adaptively Banded Smith-Waterman Algorithm for Long Reads and Its Hardware Accelerator , 2018, 2018 IEEE 29th International Conference on Application-specific Systems, Architectures and Processors (ASAP).

[9]  Hong Qu,et al.  One-dimensional pairwise CNN for the global alignment of two DNA sequences , 2015, Neurocomputing.

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

[11]  Yong Dou,et al.  Optimization schemes and performance evaluation of Smith–Waterman algorithm on CPU, GPU and FPGA , 2012, Concurr. Comput. Pract. Exp..

[12]  Yongchao Liu,et al.  SWAPHI-LS: Smith-Waterman Algorithm on Xeon Phi coprocessors for Long DNA Sequences , 2014, 2014 IEEE International Conference on Cluster Computing (CLUSTER).

[13]  Fa Zhang,et al.  A parallel Smith-Waterman algorithm based on divide and conquer , 2002, Fifth International Conference on Algorithms and Architectures for Parallel Processing, 2002. Proceedings..

[14]  Patrick Kwabena Mensah,et al.  RNS Smith-Waterman Accelerator based on the moduli set 2n, 2n-1, 2n-1-1 , 2018, 2018 IEEE 7th International Conference on Adaptive Science & Technology (ICAST).

[15]  Xin Chang,et al.  Optimization Strategies for Smith-Waterman Algorithm on FPGA Platform , 2014, 2014 International Conference on Computational Science and Computational Intelligence.

[16]  Stephen Neuendorffer,et al.  FPGA Based OpenCL Acceleration of Genome Sequencing Software , 2015 .

[17]  M. Brobbel,et al.  Acceleration of the Smith-Waterman algorithm for DNA sequence alignment using an FPGA platform , 2013 .

[18]  Armando De Giusti,et al.  SWIFOLD: Smith-Waterman implementation on FPGA with OpenCL for long DNA sequences , 2018, BMC Systems Biology.

[19]  Endri Bezati,et al.  High level synthesis of Smith-Waterman dataflow implementations , 2017, 2017 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP).

[20]  Yoshiki Yamaguchi,et al.  A Block-Based Systolic Array on an HBM2 FPGA for DNA Sequence Alignment , 2020, ARC.

[21]  D. S. Nurdin,et al.  DNA sequence alignment: A review of hardware accelerators and a new core architecture , 2016, 2016 3rd International Conference on Electronic Design (ICED).

[22]  Jaime Velasco-Medina,et al.  Hardware implementation of the Smith-Waterman algorithm using a systolic architecture , 2014, 2014 IEEE 5th Latin American Symposium on Circuits and Systems.