Reconfigurable architectures for bio-sequence database scanning on FPGAs

No abstract is available for this paper.

• Publication year

  2005

• Venue

  IEEE Transactions on Circuits and Systems - II - Express Briefs

• Publication date

  2005-12-12

• Fields of study

  Biology, Computer Science, Engineering

• Identifiers
  DOI 10.1109/TCSII.2005.853340
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar

• No claims are published for this paper.

• No concepts are published for this paper.

• The UCSC Kestrel parallel processor

  2005cited by this paper
• A Smith-Waterman Systolic Cell

  2003cited by this paper
• The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003

  2003influential reference
• Massively parallel solutions for molecular sequence analysis

  2002cited by this paper
• Gene Matching Using JBits

  2002cited by this paper
• High Speed Homology Search with FPGAs

  2001cited by this paper
• The UCSC Kestrel General Purpose Parallel Processor

  1999influential reference
• SAMBA: hardware accelerator for biological sequence comparison

  1997influential reference
• BioSCAN: a network sharable computational resource for searching biosequence databases

  1996cited by this paper
• Parallel hardware for sequence comparison and alignment

  1996cited by this paper
• Processing in Memory: The Terasys Massively Parallel PIM Array

  1995cited by this paper
• Parallel sequence comparison and alignment

  1995cited by this paper
• A SIMD solution to the sequence comparison problem on the MGAP

  1994cited by this paper
• Searching genetic databases on Splash 2

  1993cited by this paper
• Basic local alignment search tool.

  1990cited by this paper
• P-NAC: A Systolic Array for Comparing Nucleic Acid Sequences

  1987cited by this paper
• Identification of common molecular subsequences.

  1981cited by this paper

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  2022cites this paper
• Bit-Vector-Based Hardware Accelerator for DNA Alignment Tools

  2020cites this paper
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  2019cites this paper
• Dedicated Bioinformatics Analysis Hardware

  2019cites this paper
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  2018cites this paper
• A time-multiplexed FPGA overlay with linear interconnect

  2018cites this paper
• VLSI Implementation of Smith–Waterman Algorithm for Biological Sequence Scanning

  2018cites this paper
• New Trends in Computer Technologies and Applications

  2018influential citation
• Accelerated Parallel Based Distance Calculations for Live-Cell Time-Lapse Images

  2018cites this paper
• Accelerated GPU Based Protein Sequence Alignment – An optimized database sequences approach

  2017cites this paper
• The First 25 Years of the FPL Conference

  2017cites this paper
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  2017cites this paper
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  2017cites this paper
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  2017cites this paper
• Energy efficiency of sequence alignment tools - Software and hardware perspectives

  2017cites this paper
• Novel Reconfigurable Hardware Accelerator for Protein Sequence Alignment Using Smith-Waterman Algorithm

  2016cites this paper
• Parallel Optimal Pairwise Biological Sequence Comparison

  2016cites this paper
• DNA sequence alignment: A review of hardware accelerators and a new core architecture

  2016cites this paper
• DNA sequence alignment: From algorithm to systolic architecture

  2016cites this paper
• State-of-the-Art in Smith–Waterman Protein Database Search on HPC Platforms

  2016cites this paper
• GSWABE: faster GPU‐accelerated sequence alignment with optimal alignment retrieval for short DNA sequences

  2015cites this paper
• A New Processor Array Structure for Protein Sequence Alignment using Smith-Waterman Algorithm

  2015cites this paper
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  2015cites this paper
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  2015cites this paper
• Accelerating Smith-Waterman Alignment for Protein Database Search Using Frequency Distance Filtration Scheme Based on CPU-GPU Collaborative System

  2015cites this paper
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  2015cites this paper
• 3D-Stacked Many-Core Architecture for Biological Sequence Analysis Problems

  2015cites this paper
• Improving the Mapping of Smith-Waterman Sequence Database Searches onto CUDA-Enabled GPUs

  2015cites this paper
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  2014cites this paper
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  2014cites this paper
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  2014cites this paper
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  2014cites this paper
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  2014cites this paper
• MR-CUDASW - GPU accelerated Smith-Waterman algorithm for medium-length (meta)genomic data

  2014cites this paper
• Design and analysis of bioinformatics algorithms on an FPGA platform

  2014cites this paper
• Fast Sequence Alignment Method Using CUDA-enabled GPU

  2014cites this paper
• SWAPHI-LS: Smith-Waterman Algorithm on Xeon Phi coprocessors for Long DNA Sequences

  2014cites this paper
• Faster GPU-Accelerated Smith-Waterman Algorithm with Alignment Backtracking for Short DNA Sequences

  2013cites this paper
• FPGA-Based HPRC for Bioinformatics Applications

  2013cites this paper
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  2013cites this paper
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  2013cites this paper
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  2013cites this paper
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  2013cites this paper
• FPGA architecture for pairwise statistical significance estimation

  2013cites this paper
• Towards the development of a reliable reconfigurable real-time operating system on FPGAs

  2013cites this paper
• High performance reconfigurable architectures for biological sequence alignment

  2013influential citation
• Fine-grained parallel implementations for SWAMP+ Smith-Waterman alignment

  2013cites this paper
• CUDASW++ 3.0: accelerating Smith-Waterman protein database search by coupling CPU and GPU SIMD instructions

  2013cites this paper
• Opportunities from the use of FPGAs as platforms for bioinformatics algorithms

  2012cites this paper
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  2012cites this paper
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  2012cites this paper
• Profiling biological applications for parallel implementation in multicore computers

  2012cites this paper
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  2012cites this paper
• Using frequency distance filteration for reducing database search workload on GPU-based cloud service

  2012cites this paper
• Accurate Scanning of Sequence Databases with the Smith-Waterman Algorithm

  2011cites this paper
• Protein alignment algorithms with an efficient backtracking routine on multiple GPUs

  2011cites this paper
• Accelerating Smith-Waterman on Heterogeneous CPU-GPU Systems

  2011cites this paper
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  2011cites this paper
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  2011cites this paper
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  2011cites this paper
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  2011cites this paper
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  2010cites this paper
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  2010cites this paper
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  2010cites this paper
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  2010cites this paper
• CUDASW++2.0: enhanced Smith-Waterman protein database search on CUDA-enabled GPUs based on SIMT and virtualized SIMD abstractions

  2010cites this paper
• A Parallel Programming Framework for Multi-core DNA Sequence Alignment

  2010cites this paper
• A parallel FPGA design of the Smith-Waterman traceback

  2010cites this paper
• Efficient Pairwise Statistical Significance Estimation using FPGAs

  2010influential citation
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  2010cites this paper
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  2010cites this paper
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  2010cites this paper
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  2010influential citation
• High performance protein sequence database scanning on the Cell Broadband Engine

  2009influential citation
• MSA-CUDA: Multiple Sequence Alignment on Graphics Processing Units with CUDA

  2009cites this paper
• Assessment of graphics processing units for acceleration of sequence database search programs

  2009influential citation
• A framework for supporting hardware acceleration under operating system control

  2009cites this paper
• CUDASW++: optimizing Smith-Waterman sequence database searches for CUDA-enabled graphics processing units

  2009cites this paper
• Parallel reconstruction of neighbor-joining trees for large multiple sequence alignments using CUDA

  2009cites this paper
• PheGeeatHome: A Grid-Based Tool for Comparative Genomics

  2009cites this paper
• High Speed Biological Sequence Analysis With Hidden Markov Models on Reconfigurable Platforms

  2009cites this paper
• A Massively Parallel Architecture for Bioinformatics

  2009cites this paper
• Boosting data throughput for sequence database similarity searches on FPGAs using an adaptive buffering scheme

  2009cites this paper
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  2008influential citation
• CBESW: Sequence Alignment on the Playstation 3

  2008cites this paper
• Acceleration of Smith-Waterman using Recursive Variable Expansion

  2008cites this paper
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  2008influential citation
• A General Reconfigurable Architecture for the BLAST Algorithm

  2007cites this paper
• C-Based Design Methodology for FPGA Implementation of ClustalW MSA

  2007cites this paper
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  2007cites this paper
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  2007influential citation
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  2007cites this paper
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  2007cites this paper
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  2007cites this paper
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  2007cites this paper
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  2006cites this paper
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  2005cites this paper