%0 Journal Article %J IEEE/ACM Trans Comput Biol Bioinform %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 Domínguez, Andrés Tomás %A Hernández García, Vicente %A Medina Castelló, Ignacio %A Tárraga Giménez, Joaquín %A Dopazo Blázquez, Joaquín %K Algorithms %K Animals %K Computational Biology %K Computer Graphics %K Data Compression %K Drosophila melanogaster %K Genes, Insect %K Image Processing, Computer-Assisted %K Models, Genetic %K Sequence Alignment %K Sequence Analysis, DNA %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 12, when compared to CPU execution. This implementation exploits the parallelism by concurrently searching different sequences on the same reference search tree, maximizing memory locality and ensuring a symmetric access to the data. The paper describes the behavior 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 Trans Comput Biol Bioinform %V 9 %P 1245-56 %8 2012 Jul-Aug %G eng %N 4 %1 https://www.ncbi.nlm.nih.gov/pubmed/22450827?dopt=Abstract %R 10.1109/TCBB.2012.49