TY - JOUR T1 - Using GPUs for the Exact Alignment of Short-read Genetic Sequences by Means of the Burrows–Wheeler Transform. JF - IEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM Y1 - 2012 A1 - Salavert Torres, Jose A1 - Blanquer Espert, Ignacio A1 - Tomas Dominguez, Andres A1 - Hernendez, Vicente A1 - Medina, Ignacio A1 - Terraga, Joaquin A1 - Dopazo, Joaquin KW - Burrows-Wheeler transform KW - CPU execution KW - GPGPU KW - NGS AB - 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. VL - 9 UR - http://ieeexplore.ieee.org.sire.ub.edu/xpl/articleDetails.jsp?reload=true&arnumber=6175888 ER -