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Literature DB >> 20161021

Optimizing Data Intensive GPGPU Computations for DNA Sequence Alignment.

Abstract

MUMmerGPU uses highly-parallel commodity graphics processing units (GPU) to accelerate the data-intensive computation of aligning next generation DNA sequence data to a reference sequence for use in diverse applications such as disease genotyping and personal genomics. MUMmerGPU 2.0 features a new stackless depth-first-search print kernel and is 13× faster than the serial CPU version of the alignment code and nearly 4× faster in total computation time than MUMmerGPU 1.0. We exhaustively examined 128 GPU data layout configurations to improve register footprint and running time and conclude higher occupancy has greater impact than reduced latency. MUMmerGPU is available open-source at http://mummergpu.sourceforge.net.

Entities: Chemical Disease Gene Species

Year: 2009 PMID： 20161021 PMCID： PMC2749273 DOI： 10.1016/j.parco.2009.05.002

Source DB: PubMed Journal: Parallel Comput ISSN： 0167-8191 Impact factor: 0.986

8 in total

1. Fast algorithms for large-scale genome alignment and comparison.

Authors: Arthur L Delcher; Adam Phillippy; Jane Carlton; Steven L Salzberg
Journal: Nucleic Acids Res Date: 2002-06-01 Impact factor: 16.971

2. Basic local alignment search tool.

Authors: S F Altschul; W Gish; W Miller; E W Myers; D J Lipman
Journal: J Mol Biol Date: 1990-10-05 Impact factor: 5.469

3. Accelerating molecular modeling applications with graphics processors.

Authors: John E Stone; James C Phillips; Peter L Freddolino; David J Hardy; Leonardo G Trabuco; Klaus Schulten
Journal: J Comput Chem Date: 2007-12 Impact factor: 3.376

4. Next-generation sequencing outpaces expectations.

Authors: Catherine Shaffer
Journal: Nat Biotechnol Date: 2007-02-01 Impact factor: 54.908

5. The year of sequencing.

Authors: Kelly Rae Chi
Journal: Nat Methods Date: 2008-01 Impact factor: 28.547

6. A whole-genome assembly of Drosophila.

Authors: E W Myers; G G Sutton; A L Delcher; I M Dew; D P Fasulo; M J Flanigan; S A Kravitz; C M Mobarry; K H Reinert; K A Remington; E L Anson; R A Bolanos; H H Chou; C M Jordan; A L Halpern; S Lonardi; E M Beasley; R C Brandon; L Chen; P J Dunn; Z Lai; Y Liang; D R Nusskern; M Zhan; Q Zhang; X Zheng; G M Rubin; M D Adams; J C Venter
Journal: Science Date: 2000-03-24 Impact factor: 47.728

7. Alignment of whole genomes.

Authors: A L Delcher; S Kasif; R D Fleischmann; J Peterson; O White; S L Salzberg
Journal: Nucleic Acids Res Date: 1999-06-01 Impact factor: 16.971

8. High-throughput sequence alignment using Graphics Processing Units.

Authors: Michael C Schatz; Cole Trapnell; Arthur L Delcher; Amitabh Varshney
Journal: BMC Bioinformatics Date: 2007-12-10 Impact factor: 3.169

8 in total

16 in total

1. BarraCUDA - a fast short read sequence aligner using graphics processing units.

Authors: Petr Klus; Simon Lam; Dag Lyberg; Ming Sin Cheung; Graham Pullan; Ian McFarlane; Giles Sh Yeo; Brian Yh Lam
Journal: BMC Res Notes Date: 2012-01-13

2. A cellular model of amyloid precursor protein processing and amyloid-β peptide production.

Authors: Mimi P Macias; Amanda M Gonzales; Ashley L Siniard; Aaron W Walker; Jason J Corneveaux; Matthew J Huentelman; Marwan N Sabbagh; Boris Decourt
Journal: J Neurosci Methods Date: 2013-12-12 Impact factor: 2.390

3. Transcriptome and in Vitro Differentiation Profile of Human Embryonic Stem Cell Derived NKX2.1-Positive Neural Progenitors.

Authors: Christopher Y Chen; Alex Plocik; Nickesha C Anderson; Daniel Moakley; Trinithas Boyi; Carolyn Dundes; Chelsea Lassiter; Brenton R Graveley; Laura Grabel
Journal: Stem Cell Rev Rep Date: 2016-12 Impact factor: 5.739

10. Increased whole blood FFA2/GPR43 receptor expression is associated with increased 30-day survival in patients with sepsis.

Authors: Zyad J Carr; Andry Van De Louw; Graham Fehr; Jialiu D Li; Allen Kunselman; Victor Ruiz-Velasco
Journal: BMC Res Notes Date: 2018-01-16

Optimizing Data Intensive GPGPU Computations for DNA Sequence Alignment.

1. Fast algorithms for large-scale genome alignment and comparison.

2. Basic local alignment search tool.

3. Accelerating molecular modeling applications with graphics processors.

4. Next-generation sequencing outpaces expectations.

5. The year of sequencing.

6. A whole-genome assembly of Drosophila.

7. Alignment of whole genomes.

8. High-throughput sequence alignment using Graphics Processing Units.

1. BarraCUDA - a fast short read sequence aligner using graphics processing units.

2. A cellular model of amyloid precursor protein processing and amyloid-β peptide production.

3. Transcriptome and in Vitro Differentiation Profile of Human Embryonic Stem Cell Derived NKX2.1-Positive Neural Progenitors.

4. GPR56 contributes to the development of acute myeloid leukemia in mice.

5. Characterization of the transcriptomes of Atoh1-induced hair cells in the mouse cochlea.

6. Protein neddylation as a therapeutic target in pulmonary and extrapulmonary small cell carcinomas.

7. Fast and accurate protein substructure searching with simulated annealing and GPUs.

8. A practical comparison of de novo genome assembly software tools for next-generation sequencing technologies.

9. Protein-ligand binding region prediction (PLB-SAVE) based on geometric features and CUDA acceleration.

10. Increased whole blood FFA2/GPR43 receptor expression is associated with increased 30-day survival in patients with sepsis.