The recent availability of new, less expensive high-throughput DNA sequencing technologies has yielded a dramatic increase in the volume of sequence data that must be analyzed. by University of Maryland researchers Michael Schatz, Cole Trapnell, Art Delcher, and Amitabh Varshney describes MUMmerGPU, an open-source high-throughput parallel pairwise local sequence alignment program that runs on GPUs. MUMmerGPU uses the new Compute Unified Device Architecture (CUDA) from nVidia to align multiple query sequences against a single reference sequence stored as a suffix tree. By processing the queries in parallel on the graphics card, MUMmerGPU achieves more than a 10-fold speedup over a serial CPU version of the sequence alignment kernel, despite the very low arithmetic intensity of the task. (High-throughput sequence alignment using Graphics Processing Units, Schatz, M.C., Trapnell, C., Delcher, A.L., Varshney, A. (2007), BMC Bioinformatics 8:474.)