Journal of
Bioinformatics and Sequence Analysis

  • Abbreviation: J. Bioinform. Seq. Anal.
  • Language: English
  • ISSN: 2141-2464
  • DOI: 10.5897/JBSA
  • Start Year: 2009
  • Published Articles: 46

Full Length Research Paper

Evaluating the computing efficiencies (specificity and sensitivity) of graphics processing unit (GPU)-accelerated DNA sequence alignment tools against central processing unit (CPU) alignment tool

Shrikant Pawar
  • Shrikant Pawar
  • Department of Computer Science, Georgia State University, 34 Peachtree Street, 30303, Atlanta, GA, USA.
  • Google Scholar
Aditya Stanam
  • Aditya Stanam
  • College of Public Health, The University of Iowa, UI Research Park, #219 IREH, 52242-5000, Iowa City, Iowa, USA.
  • Google Scholar
Ying Zhu
  • Ying Zhu
  • Creative Media Industries Institute and Department of Computer Science, Georgia State University, 34 Peachtree Street, 30303, Atlanta, GA, USA.
  • Google Scholar


  •  Received: 18 March 2018
  •  Accepted: 27 July 2018
  •  Published: 31 July 2018

References

Chi-Man L, Ruibang L, Tak-Wah L (2014). GPU-Accelerated BWT Construction for Large Collection of Short Reads. CiteSeer. 2014.

 

Jochen B, Tobias J, Daniel D, Sebastian J, Jörn K, Jens S, Alexander G (2011). Exact and complete short-read alignment to microbial genomes using Graphics Processing Unit programming. Bioinformatics 27(10):1351-1358.
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Li H (2008a). Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Research 18:1851-1858.
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Li R (2008b). SOAP: short oligonucleotide alignment program. Bioinformatics 24:713-714.
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Langdon WB, Lam BY, Petke J, Harman M (2015). Improving CUDA DNA Analysis Software with Genetic Programming. Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation - GECCO '15.
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Petr Klus K, Simon L, Dag L, Ming SC, Graham P, Ian M, Giles SHY, Brian YHL (2012). BarraCUDA - a fast short read sequence aligner using graphics processing units. BMC Research Notes 5:27.
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Wang J, Wang W, Li R, Li Y, Tian G, Goodman L, Fan W, Zhang J, Li J, Zhang J, Guo Y (2008). The diploid genome sequence of an Asian individual. Nature 456(7218):60.
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Yongchao L, Bertil S, Douglas LM (2012). CUSHAW: a CUDA compatible short read aligner to large genomes based on the Burrows–Wheeler transform. Bioinformatics 28(14):1830-1837.
Crossref