%0 Journal Article %J IEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM %D 2012 %T Using GPUs for the Exact Alignment of Short-read Genetic Sequences by Means of the Burrows–Wheeler Transform. %A Salavert Torres, Jose %A Blanquer Espert, Ignacio %A Tomas Dominguez, Andres %A Hernendez, Vicente %A Medina, Ignacio %A Terraga, Joaquin %A Dopazo, Joaquin %K Burrows-Wheeler transform %K CPU execution %K GPGPU %K NGS %X General Purpose Graphic Processing Units (GPGPUs) constitute an inexpensive resource for computing-intensive applications that could exploit an intrinsic fine-grain parallelism. This paper presents the design and implementation in GPGPUs of an exact alignment tool for nucleotide sequences based on the Burrows-Wheeler Transform. We compare this algorithm with state-of-the-art implementations of the same algorithm over standard CPUs, and considering the same conditions in terms of I/O. Excluding disk transfers, the implementation of the algorithm in GPUs shows a speedup larger than 12x, when compared to CPU execution. This implementation exploits the parallelism by concurrently searching different sequences on the same reference search tree, maximising memory locality and ensuring a symmetric access to the data. The article describes the behaviour of the algorithm in GPU, showing a good scalability in the performance, only limited by the size of the GPU inner memory. %B IEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM %V 9 %P 1245-1256 %8 2012 Mar 20 %G eng %U http://ieeexplore.ieee.org.sire.ub.edu/xpl/articleDetails.jsp?reload=true&arnumber=6175888 %R 10.1109/TCBB.2012.49