02206nas a2200349 4500008004100000022001400041245011400055210006900169260001700238300001200255490000600267520098700273653001501260653001201275653002601287653002201313653002101335653002801356653001801384653004001402653002001442653002301462653002701485100002701512700003001539700003201569700003301601700003101634700003301665700003201698856012601730 2012 eng d a1557-996400aUsing GPUs for the exact alignment of short-read genetic sequences by means of the Burrows-Wheeler transform.0 aUsing GPUs for the exact alignment of shortread genetic sequence c2012 Jul-Aug a1245-560 v93 a
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.
10aAlgorithms10aAnimals10aComputational Biology10aComputer Graphics10aData Compression10aDrosophila melanogaster10aGenes, Insect10aImage Processing, Computer-Assisted10aModels, Genetic10aSequence Alignment10aSequence Analysis, DNA1 aTorres, Jose, Salavert1 aEspert, Ignacio, Blanquer1 aDomínguez, Andrés, Tomás1 aGarcía, Vicente, Hernández1 aCastelló, Ignacio, Medina1 aGiménez, Joaquín, Tárraga1 aBlázquez, Joaquín, Dopazo uhttp://clinbioinfosspa.es/content/using-gpus-exact-alignment-short-read-genetic-sequences-means-burrows-wheeler-transform