@article {900, title = {Using GPUs for the Exact Alignment of Short-read Genetic Sequences by Means of the Burrows{\textendash}Wheeler Transform.}, journal = {IEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM}, volume = {9}, number = {4}, year = {2012}, month = {2012 Mar 20}, pages = {1245-1256}, abstract = {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.}, keywords = {Burrows-Wheeler transform, CPU execution, GPGPU, NGS}, issn = {1557-9964}, doi = {10.1109/TCBB.2012.49}, url = {http://ieeexplore.ieee.org.sire.ub.edu/xpl/articleDetails.jsp?reload=true\&arnumber=6175888}, author = {Salavert Torres, Jose and Blanquer Espert, Ignacio and Tomas Dominguez, Andres and Hernendez, Vicente and Medina, Ignacio and Terraga, Joaquin and Dopazo, Joaquin} }