CUDASW++: optimizing Smith-Waterman sequence database searches for CUDA-enabled graphics processing units (Q30488136)

4 October 2017

CUDASW++: optimizing Smith-Waterman sequence database searches for CUDA-enabled graphics processing units (English)

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4 October 2017

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Yongchao Liu

1

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4 October 2017

Douglas L Maskell

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2

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4 October 2017

Bertil Schmidt

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3

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4 October 2017

6 May 2009

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4 October 2017

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4 October 2017

2

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4 October 2017

73

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SWPS3 - fast multi-threaded vectorized Smith-Waterman for IBM Cell/B.E. and x86/SSE2

4 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2694204

CBESW: sequence alignment on the Playstation 3.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2694204

CUDA compatible GPU cards as efficient hardware accelerators for Smith-Waterman sequence alignment

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2694204

160-fold acceleration of the Smith-Waterman algorithm using a field programmable gate array (FPGA).

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2694204

Striped Smith-Waterman speeds database searches six times over other SIMD implementations

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2694204

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2694204

Using video-oriented instructions to speed up sequence comparison

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2694204

Identification of common molecular subsequences

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2694204

Improved tools for biological sequence comparison

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2694204

Basic local alignment search tool

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2694204

Using reconfigurable hardware to accelerate multiple sequence alignment with ClustalW.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2694204

Six-fold speed-up of Smith-Waterman sequence database searches using parallel processing on common microprocessors

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2694204

An improved algorithm for matching biological sequences.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2694204

26 November 2018

Identifiers

DOI

10.1186/1756-0500-2-73

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Dimensions Publication ID

4 October 2017

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1 reference

4 October 2017

PubMed publication ID

19416548

1 reference