Graphics processing units in bioinformatics, computational biology and systems biology
Abstract Several studies in Bioinformatics, Computational Biology and Systems Biology rely
on the definition of physico-chemical or mathematical models of biological systems at …
on the definition of physico-chemical or mathematical models of biological systems at …
GPU-BLAST: using graphics processors to accelerate protein sequence alignment
PD Vouzis, NV Sahinidis - Bioinformatics, 2011 - academic.oup.com
Abstract Motivation: The Basic Local Alignment Search Tool (BLAST) is one of the most
widely used bioinformatics tools. The widespread impact of BLAST is reflected in over 53 …
widely used bioinformatics tools. The widespread impact of BLAST is reflected in over 53 …
RADAR: A 3D-ReRAM based DNA alignment accelerator architecture
Next Generation Sequencing (NGS) technology has become an indispensable tool for
studying genomics, resulting in an exponentially growth of biological data. Booming data …
studying genomics, resulting in an exponentially growth of biological data. Booming data …
Environmental bio-monitoring with high-throughput sequencing
J Wang, PA McLenachan, PJ Biggs… - Briefings in …, 2013 - academic.oup.com
There is much interest in using high-throughput DNA sequencing methodology to monitor
microorganisms, complex plant and animal communities. However, there are experimental …
microorganisms, complex plant and animal communities. However, there are experimental …
NCBI BLASTP on high-performance reconfigurable computing systems
A Mahram, MC Herbordt - ACM Transactions on Reconfigurable …, 2015 - dl.acm.org
The BLAST sequence alignment program is a central application in bioinformatics. The de
facto standard version, NCBI BLAST, uses complex heuristics that make it challenging to …
facto standard version, NCBI BLAST, uses complex heuristics that make it challenging to …
G-BLASTN: accelerating nucleotide alignment by graphics processors
Motivation: Since 1990, the basic local alignment search tool (BLAST) has become one of
the most popular and fundamental bioinformatics tools for sequence similarity searching …
the most popular and fundamental bioinformatics tools for sequence similarity searching …
Space efficient sequence alignment for sram-based computing: X-drop on the graphcore IPU
Dedicated accelerator hardware has become essential for processing AI-based workloads,
leading to the rise of novel accelerator architectures. Furthermore, fundamental differences …
leading to the rise of novel accelerator architectures. Furthermore, fundamental differences …
CLUS_GPU-BLASTP: Accelerated protein sequence alignment using GPU-enabled cluster
Abstract Basic Local Alignment Search Tool (BLAST) is one of the most frequently used
algorithms for bioinformatics applications. In this paper, an accelerated implementation of …
algorithms for bioinformatics applications. In this paper, an accelerated implementation of …
cublastp: Fine-grained parallelization of protein sequence search on cpu+ gpu
BLAST, short for Basic Local Alignment Search Tool, is a ubiquitous tool used in the life
sciences for pairwise sequence search. However, with the advent of next-generation …
sciences for pairwise sequence search. However, with the advent of next-generation …
Using GPUs for the exact alignment of short-read genetic sequences by means of the Burrows-Wheeler transform
JS Torres, IB Espert, AT Dominguez… - IEEE/ACM …, 2012 - ieeexplore.ieee.org
General Purpose Graphic Processing Units (GPGPUs) constitute an inexpensive resource
for computing-intensive applications that could exploit an intrinsic fine-grain parallelism. This …
for computing-intensive applications that could exploit an intrinsic fine-grain parallelism. This …