Darwin: A genomics co-processor provides up to 15,000 x acceleration on long read assembly

Y Turakhia, G Bejerano, WJ Dally - ACM SIGPLAN Notices, 2018 - dl.acm.org
Genomics is transforming medicine and our understanding of life in fundamental ways.
Genomics data, however, is far outpacing Moore» s Law. Third-generation sequencing …

[图书][B] Reconfigurable computing: Accelerating computation with field-programmable gate arrays

MB Gokhale, PS Graham - 2006 - books.google.com
A one-of-a-kind survey of the field of Reconfigurable Computing Gives a comprehensive
introduction to a discipline that offers a 10X-100X acceleration of algorithms over …

Hardware acceleration of long read pairwise overlapping in genome sequencing: A race between fpga and gpu

L Guo, J Lau, Z Ruan, P Wei… - 2019 IEEE 27th Annual …, 2019 - ieeexplore.ieee.org
In genome sequencing, it is a crucial but time-consuming task to detect potential overlaps
between any pair of the input reads, especially those that are ultra-long. The state-of-the-art …

A highly parameterized and efficient FPGA-based skeleton for pairwise biological sequence alignment

K Benkrid, Y Liu, AS Benkrid - IEEE Transactions on Very Large …, 2009 - ieeexplore.ieee.org
This paper presents the design and implementation of the most parameterisable field-
programmable gate array (FPGA)-based skeleton for pairwise biological sequence …

Using reconfigurable hardware to accelerate multiple sequence alignment with ClustalW

T Oliver, B Schmidt, D Nathan, R Clemens… - …, 2005 - academic.oup.com
Aligning hundreds of sequences using progressive alignment tools such as ClustalW
requires several hours on state-of-the-art workstations. We present a new approach to …

Bio-sequence database scanning on a GPU

W Liu, B Schmidt, G Voss, A Schroder… - … Parallel & Distributed …, 2006 - ieeexplore.ieee.org
Protein sequences with unknown functionality are often compared to a set of known
sequences to detect functional similarities. Efficient dynamic programming algorithms exist …

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 …

Mercury BLASTP: Accelerating protein sequence alignment

A Jacob, J Lancaster, J Buhler, B Harris… - ACM Transactions on …, 2008 - dl.acm.org
Large-scale protein sequence comparison is an important but compute-intensive task in
molecular biology. BLASTP is the most popular tool for comparative analysis of protein …

Hyper customized processors for bio-sequence database scanning on FPGAs

T Oliver, B Schmidt, D Maskell - Proceedings of the 2005 ACM/SIGDA …, 2005 - dl.acm.org
Protein sequences with unknown functionality are often compared to a set of known
sequences to detect functional similarities. Efficient dynamic-programming algorithms exist …

Reconfigurable architectures for bio-sequence database scanning on FPGAs

TF Oliver, B Schmidt, DL Maskell - IEEE Transactions on …, 2005 - ieeexplore.ieee.org
Protein sequences with unknown functionality are often compared to a set of known
sequences to detect functional similarities. Efficient dynamic-programming algorithms exist …