Table 2.
GPU applications for bioinformatics.
| CATEGORY | APPLICATION | DESCRIPTION |
|---|---|---|
| Alignment | CUSHAW110 | Short read alignment based on the Burrows-Wheeler transform (BWT111) and the Ferragina-Manzini index112 |
| SOAP3-dp113 | Short read alignment based on BWT with native BAM support | |
| Proteomics | FastPaSS114 | Spectra matching using spectral library searching implemented in CUDA |
| Tempest115 | Spectral matching using GPU-CPU | |
| Motif Discovery | GPUmotif116 | Motif scan and de novo motif finding using GPU |
| Epigenetics | GPU-BSM117 | GPU based tool for mapping whole genome bisulfite sequencing reads and estimating methylation levels |
| Systems Biology (see Ref.118 for a review) | ABC-SysBio119 | Simulate models written in the Systems Biology Markup Language (SBML120) format |
| PMCGPU121,122 | Parallel simulators for Membrane Computing on the GPU | |
| Genome-wide Inference | permGPU123 | Permutation resampling analysis for binary, quantitative, and censored time-to-event outcomes |