title: gCUP: rapid GPU-based HIV-1 co-receptor usage prediction for next-generation sequencing.
abstract: CONCLUSIONS
  Next-generation sequencing (NGS) has a large potential in HIV diagnostics, and genotypic prediction models have been developed and successfully tested in the recent years. However, albeit being highly accurate, these computational models lack computational efficiency to reach their full potential. In this study, we demonstrate the use of graphics processing units (GPUs) in combination with a computational prediction model for HIV tropism. Our new model named gCUP, parallelized and optimized for GPU, is highly accurate and can classify >175 000 sequences per second on an NVIDIA GeForce GTX 460. The computational efficiency of our new model is the next step to enable NGS technologies to reach clinical significance in HIV diagnostics. Moreover, our approach is not limited to HIV tropism prediction, but can also be easily adapted to other settings, e.g. drug resistance prediction.
  
  
  METHODS
  The source code can be downloaded at http://www.heiderlab.de
  
  
  BACKGROUND
  d.heider@wz-straubing.de.
authors.affiliation: Institute of Computer Science, University of Muenster, 48149 Muenster and Department of Bioinformatics, University of Applied Sciences Weihenstephan-Triesdorf, 94315 Straubing, Germany.
authors.forename: Michael
authors.initials: M
authors.lastname: Olejnik
authors.affiliation: Institute of Computer Science, University of Muenster, 48149 Muenster and Department of Bioinformatics, University of Applied Sciences Weihenstephan-Triesdorf, 94315 Straubing, Germany.
authors.forename: Michel
authors.initials: M
authors.lastname: Steuwer
authors.affiliation: Institute of Computer Science, University of Muenster, 48149 Muenster and Department of Bioinformatics, University of Applied Sciences Weihenstephan-Triesdorf, 94315 Straubing, Germany.
authors.forename: Sergei
authors.initials: S
authors.lastname: Gorlatch
authors.affiliation: Institute of Computer Science, University of Muenster, 48149 Muenster and Department of Bioinformatics, University of Applied Sciences Weihenstephan-Triesdorf, 94315 Straubing, Germany.
authors.forename: Dominik
authors.initials: D
authors.lastname: Heider
mesh_terms: D015497:HIV-1 / Q000235:genetics / Q000502:physiology*; D059014:High-Throughput Nucleotide Sequencing; D015728:Receptors, HIV / Q000737:chemistry / Q000235:genetics*; D012984:Software; D056189:Viral Tropism
chemical_list: D015728:Receptors, HIV