Biohd: an efficient genome sequence search platform using hyperdimensional memorization
In this paper, we propose BioHD, a novel genomic sequence searching platform based on
Hyper-Dimensional Computing (HDC) for hardware-friendly computation. BioHD transforms …
Hyper-Dimensional Computing (HDC) for hardware-friendly computation. BioHD transforms …
[HTML][HTML] SWIFOLD: Smith-Waterman implementation on FPGA with OpenCL for long DNA sequences
Abstract Background The Smith-Waterman (SW) algorithm is the best choice for searching
similar regions between two DNA or protein sequences. However, it may become …
similar regions between two DNA or protein sequences. However, it may become …
Finder: Accelerating fm-index-based exact pattern matching in genomic sequences through reram technology
Genomics is the critical key to enabling precision medicine, ensuring global food security
and enforcing wildlife conservation. The massive genomic data produced by various …
and enforcing wildlife conservation. The massive genomic data produced by various …
Fpga hpc using opencl: Case study in 3d fft
A Sanaullah, MC Herbordt - … of the 9th International Symposium on …, 2018 - dl.acm.org
FPGAs have typically achieved high speedups for 3D Fast Fourier Transforms (FFTs) due to
the presence of hard floating point units, low latency specialized pipelines, and support for …
the presence of hard floating point units, low latency specialized pipelines, and support for …
Exma: A genomics accelerator for exact-matching
Genomics is the foundation of precision medicine, global food security and virus
surveillance. Exact-match is one of the most essential operations widely used in almost …
surveillance. Exact-match is one of the most essential operations widely used in almost …
Fpga acceleration of sequence alignment: A survey
Genomics is changing our understanding of humans, evolution, diseases, and medicines to
name but a few. As sequencing technology is developed collecting DNA sequences takes …
name but a few. As sequencing technology is developed collecting DNA sequences takes …
Unlocking performance-programmability by penetrating the intel FPGA OpenCL toolflow
A Sanaullah, MC Herbordt - 2018 IEEE High Performance …, 2018 - ieeexplore.ieee.org
Improved support for OpenCL has been an important step towards the mainstream adoption
of FPGAs as compute resources. Current research has shown, however, that …
of FPGAs as compute resources. Current research has shown, however, that …
Parallel fine-grained comparison of long dna sequences in homogeneous and heterogeneous gpu platforms with pruning
The parallelization of Smith-Waterman (SW) sequence comparison tools for long DNA
sequences has been a big challenge over the years, requesting the use of several devices …
sequences has been a big challenge over the years, requesting the use of several devices …
Asw: accelerating Smith–Waterman algorithm on coupled CPU–GPU architecture
Smith–Waterman algorithm (SW) is a popular dynamic programming algorithm widely used
in bioinformatics for local biological sequence alignment. Due to the O (n^ 2) O (n 2) high …
in bioinformatics for local biological sequence alignment. Due to the O (n^ 2) O (n 2) high …
Implementation of hybrid alignment algorithm for protein database search on the SW26010 many-core processor
H Zhang, Y Fu, LB Feng, Y Zhang, R Hua - IEEE Access, 2019 - ieeexplore.ieee.org
In biological research, biology sequence alignment algorithm aims to find similarities
between sequences. As the size of biological database increases exponentially, the …
between sequences. As the size of biological database increases exponentially, the …