Efficient architecture-aware acceleration of BWA-MEM for multicore systems
Innovations in Next-Generation Sequencing are enabling generation of DNA sequence data
at ever faster rates and at very low cost. For example, the Illumina NovaSeq 6000 sequencer …
at ever faster rates and at very low cost. For example, the Illumina NovaSeq 6000 sequencer …
[HTML][HTML] HH-suite3 for fast remote homology detection and deep protein annotation
Background HH-suite is a widely used open source software suite for sensitive sequence
similarity searches and protein fold recognition. It is based on pairwise alignment of profile …
similarity searches and protein fold recognition. It is based on pairwise alignment of profile …
Fast gap-affine pairwise alignment using the wavefront algorithm
Motivation Pairwise alignment of sequences is a fundamental method in modern molecular
biology, implemented within multiple bioinformatics tools and libraries. Current advances in …
biology, implemented within multiple bioinformatics tools and libraries. Current advances in …
[HTML][HTML] CUDASW++ 3.0: accelerating Smith-Waterman protein database search by coupling CPU and GPU SIMD instructions
Background The maximal sensitivity for local alignments makes the Smith-Waterman
algorithm a popular choice for protein sequence database search based on pairwise …
algorithm a popular choice for protein sequence database search based on pairwise …
[HTML][HTML] Faster Smith-Waterman database searches with inter-sequence SIMD parallelisation
T Rognes - BMC bioinformatics, 2011 - Springer
Abstract Background The Smith-Waterman algorithm for local sequence alignment is more
sensitive than heuristic methods for database searching, but also more time-consuming. The …
sensitive than heuristic methods for database searching, but also more time-consuming. The …
[HTML][HTML] CUDASW++: optimizing Smith-Waterman sequence database searches for CUDA-enabled graphics processing units
Abstract Background The Smith-Waterman algorithm is one of the most widely used tools for
searching biological sequence databases due to its high sensitivity. Unfortunately, the Smith …
searching biological sequence databases due to its high sensitivity. Unfortunately, the Smith …
Medal: Scalable dimm based near data processing accelerator for dna seeding algorithm
Computational genomics has proven its great potential to support precise and customized
health care. However, with the wide adoption of the Next Generation Sequencing (NGS) …
health care. However, with the wide adoption of the Next Generation Sequencing (NGS) …
[HTML][HTML] CUDASW++ 2.0: enhanced Smith-Waterman protein database search on CUDA-enabled GPUs based on SIMT and virtualized SIMD abstractions
Background Due to its high sensitivity, the Smith-Waterman algorithm is widely used for
biological database searches. Unfortunately, the quadratic time complexity of this algorithm …
biological database searches. Unfortunately, the quadratic time complexity of this algorithm …
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 …
[HTML][HTML] Computational strategies for scalable genomics analysis
The revolution in next-generation DNA sequencing technologies is leading to explosive data
growth in genomics, posing a significant challenge to the computing infrastructure and …
growth in genomics, posing a significant challenge to the computing infrastructure and …