TY - JOUR T1 - Using GPUs for the exact alignment of short-read genetic sequences by means of the Burrows-Wheeler transform. JF - IEEE/ACM Trans Comput Biol Bioinform Y1 - 2012 A1 - Salavert Torres, Jose A1 - Blanquer Espert, Ignacio A1 - Domínguez, Andrés Tomás A1 - Hernández García, Vicente A1 - Medina Castelló, Ignacio A1 - Tárraga Giménez, Joaquín A1 - Dopazo Blázquez, Joaquín KW - Algorithms KW - Animals KW - Computational Biology KW - Computer Graphics KW - Data Compression KW - Drosophila melanogaster KW - Genes, Insect KW - Image Processing, Computer-Assisted KW - Models, Genetic KW - Sequence Alignment KW - Sequence Analysis, DNA 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 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.

VL - 9 IS - 4 U1 - https://www.ncbi.nlm.nih.gov/pubmed/22450827?dopt=Abstract ER -