Parallel hardware for sequence comparison and alignment
R Hughey - Bioinformatics, 1996 - academic.oup.com
Sequence comparison, a vital research tool in computational biology, is based on a simple
O (n2) algorithm that easily maps to a linear array of processors. This paper reviews and …
O (n2) algorithm that easily maps to a linear array of processors. This paper reviews and …
Race logic: A hardware acceleration for dynamic programming algorithms
We propose a novel computing approach, dubbed" Race Logic", in which information,
instead of being represented as logic levels, as is done in conventional logic, is represented …
instead of being represented as logic levels, as is done in conventional logic, is represented …
Searching genetic databases on Splash 2
DT Hoang - [1993] Proceedings IEEE Workshop on FPGAs for …, 1993 - ieeexplore.ieee.org
The author describes two systolic arrays for computing the edit distance between two
genetic sequences using a well-known dynamic programming algorithm. The systolic arrays …
genetic sequences using a well-known dynamic programming algorithm. The systolic arrays …
A Smith-Waterman systolic cell
CW Yu, KH Kwong, KH Lee, PHW Leong - Field Programmable Logic and …, 2003 - Springer
With an aim to understand the information encoded by DNA sequences, databases
containing large amount of DNA sequence information are frequently compared and …
containing large amount of DNA sequence information are frequently compared and …
Implementation of the Smith-Waterman algorithm on a reconfigurable supercomputing platform
An innovative reconfigurable supercomputing platform--XD1000 is developed by
XtremeData Inc. to exploit the rapid progress of FPGA technology and the high-performance …
XtremeData Inc. to exploit the rapid progress of FPGA technology and the high-performance …
FPGASW: accelerating large-scale Smith–Waterman sequence alignment application with backtracking on FPGA linear systolic array
X Fei, Z Dan, L Lina, M Xin, Z Chunlei - … Sciences: Computational Life …, 2018 - Springer
Abstract The Smith–Waterman (SW) algorithm based on dynamic programming is a well-
known classical method for high precision sequence matching and has become the gold …
known classical method for high precision sequence matching and has become the gold …
Compiler generated systolic arrays for wavefront algorithm acceleration on FPGAs
B Buyukkurt, WA Najj - 2008 International Conference on Field …, 2008 - ieeexplore.ieee.org
Wavefront algorithms, such as the Smith-Waterman algorithm, are commonly used in
bioinformatics for exact local and global sequence alignment. These algorithms are highly …
bioinformatics for exact local and global sequence alignment. These algorithms are highly …
[PDF][PDF] Reconfigurable systems for sequence alignment and for general dynamic programming
RP Jacobi, M Ayala-Rincón, LGA Carvalho… - Genetics and …, 2005 - funpecrp.com.br
Reconfigurable systolic arrays can be adapted to efficiently resolve a wide spectrum of
computational problems; parallelism is naturally explored in systolic arrays and …
computational problems; parallelism is naturally explored in systolic arrays and …
Optimization schemes and performance evaluation of Smith–Waterman algorithm on CPU, GPU and FPGA
D Zou, Y Dou, F Xia - Concurrency and Computation: Practice …, 2012 - Wiley Online Library
With fierce competition between CPU and graphics processing unit (GPU) platforms,
performance evaluation has become the focus of various sectors. In this paper, we take a …
performance evaluation has become the focus of various sectors. In this paper, we take a …
A survey of FPGAs for acceleration of high performance computing and their application to computational molecular biology
T Ramdas, G Egan - TENCON 2005-2005 IEEE Region 10 …, 2005 - ieeexplore.ieee.org
Molecular biocomputation workflows traditionally involve days of compute time to align
DNA/protein sequences. Custom computing machines (CCMs) provide a means to …
DNA/protein sequences. Custom computing machines (CCMs) provide a means to …