Coupling SIMD and SIMT architectures to boost performance of a phylogeny-aware alignment kernel. (Q34372805)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22876807%20AND%20SRC:MED&resulttype=core&format=json

10 February 2020

title

Coupling SIMD and SIMT architectures to boost performance of a phylogeny-aware alignment kernel (English)

1 reference

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10 February 2020

1 reference

1

1 reference

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10 February 2020

author name string

Simon A Berger

series ordinal

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22876807%20AND%20SRC:MED&resulttype=core&format=json

10 February 2020

Alexandros Stamatakis

series ordinal

3

1 reference

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10 February 2020

publication date

9 August 2012

1 reference

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10 February 2020

1 reference

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10 February 2020

volume

13

1 reference

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10 February 2020

page(s)

196

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Creative Commons Attribution 2.0 Generic

10 February 2020

copyright license

start time

9 August 2012

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

1 reference

April 2022 Public Data File from Crossref

cites work

Faster Smith-Waterman database searches with inter-sequence SIMD parallelisation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3496624

CUDASW++2.0: enhanced Smith-Waterman protein database search on CUDA-enabled GPUs based on SIMT and virtualized SIMD abstractions

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3496624

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3496624

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3496624

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3496624

MAFFT version 5: improvement in accuracy of multiple sequence alignment

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3496624

MUSCLE: multiple sequence alignment with high accuracy and high throughput

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3496624

Profile hidden Markov models

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3496624

Using video-oriented instructions to speed up sequence comparison

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3496624

Construction of phylogenetic trees

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3496624

SEPP: SATé-enabled phylogenetic placement

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3496624

Aligning short reads to reference alignments and trees

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3496624

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

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3496624

27 October 2018

Identifiers

DOI

10.1186/1471-2105-13-196

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22876807%20AND%20SRC:MED&resulttype=core&format=json

journals/bmcbi/AlachiotisBS12

10 February 2020

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

Dimensions Publication ID

28 January 2021

0 references

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22876807%20AND%20SRC:MED&resulttype=core&format=json

10 February 2020

PubMed publication ID

22876807

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22876807%20AND%20SRC:MED&resulttype=core&format=json