@article {4,
	title = {Using GPUs for the Exact Alignment of Short-Read Genetic Sequences by Means of the Burrows-Wheeler Transform},
	journal = {IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)},
	volume = {9},
	year = {2012},
	month = {2012},
	chapter = {1245},
	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 12{\times}, 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.},
	issn = {1545-5963},
	doi = {10.1109/TCBB.2012.49},
	url = {http://dl.acm.org/citation.cfm?id=2223945},
	author = {Jose Salavert Torres and Ignacio Blanquer Espert and Andres Tomas Dominguez and Vicente Hernendez and Medina, Ignacio and Joaquin Terraga and Dopazo, Joaqu{\'\i}n}
}
