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Liang-Tsung Huang, Chao-Chin Wu, Lien-Fu Lai, Yun-Ju Li
Sequence alignment lies at heart of the bioinformatics.The Smith-Waterman algorithm is one of the key sequence search algorithms and has gained popularity due to improved implementations and rapidly increasing compute power. Recently, the Smith-Waterman algorithm has been successfully mapped onto the emerging general-purpose graphics processing units (GPUs). In this paper, we focused on how to […]
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Yucheng Zhu
The Intel Xeon Phi coprocessor is a new choice for the high performance computing industry and it needs to be tested. In this thesis, we compared the difference in performance between the Xeon Phi and the GPU. The Smith-Waterman algorithm is a widely used algorithm for solving the sequence alignment problem. We implemented two versions […]
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Amadou Chaibou, Oumarou Sie
In this paper, we present parallel programming approaches to calculate the values of the cells in matrix’s scoring used in the Smith-Waterman’s algorithm for sequence alignment. This algorithm, well known in bioinformatics for its applications, is unfortunately time-consuming on a serial computer. We use formulation based on anti-diagonals structure of data. This representation focuses on […]
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Avadhesh Pratap Singh, Dhirendra Pratap Singh
K-shortest path algorithm is generalization of the shortest path algorithm. K-shortest path is used in various fields like sequence alignment problem in molecular bioinformatics, robot motion planning, path finding in gene network where speed to calculate paths plays a vital role. Parallel implementation is one of the best ways to fulfill the requirement of these […]
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W. B. Langdon, Brian Yee Hong Lam
BarraCUDA is a C program which uses the BWA algorithm in parallel with nVidia CUDA to align short next generation DNA sequences against a reference genome. The genetically improved (GI) code is up to three times faster on short paired end reads from The 1000 Genomes Project and 60 percent more accurate on a short […]
Sven Warris, Feyruz Yalcin, Katherine J. L. Jackson, Jan Peter Nap
MOTIVATION: To obtain large-scale sequence alignments in a fast and flexible way is an important step in the analyses of next generation sequencing data. Applications based on the Smith-Waterman (SW) algorithm are often either not fast enough, limited to dedicated tasks or not sufficiently accurate due to statistical issues. Current SW implementations that run on […]
H.A. Du Nguyen, Zaid Al-Ars, Georgios Smaragdos, Christos Strydis
The Inferior Olive (IO) in the brain, in conjunction with the cerebellum, is responsible for crucial sensorimotor-integration functions in humans. In this paper, we simulate a computationally challenging IO neuron model consisting of three compartments per neuron in a network arrangement on GPU platforms. Several GPU platforms of the two latest NVIDIA GPU architectures (Fermi, […]
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Benjamin Schmid, Jan Huisken
In light-sheet microscopy, overall image content and resolution are improved by acquiring and fusing multiple views of the sample from different directions. State-of-the-art multi-view (MV) deconvolution employs the point spread functions (PSF) of the different views to simultaneously fuse and deconvolve the images in 3D, but processing takes a multiple of the acquisition time and […]
Richard Wilton, Tamas Budavari, Ben Langmead, Sarah J. Wheelan, Steven L. Salzberg, Alexander S. Szalay
When computing alignments of DNA sequences to a large genome, a key element in achieving high processing throughput is to prioritize locations in the genome where high-scoring mappings might be expected. We formulated this task as a series of list-processing operations that can be efficiently performed on graphics processing unit (GPU) hardware.We followed this approach […]
Johannes Koster
The analysis of next-generation sequencing (NGS) data is a major topic in bioinformatics: short reads obtained from DNA, the molecule encoding the genome of living organisms, are processed to provide insight into biological or medical questions. This thesis provides novel solutions to major topics within the analysis of NGS data, focusing on parallelization, scalability and […]
Dzmitry Razmyslovich, Guillermo Marcus, Markus Gipp, Marc Zapatka, Andreas Szillus
In this paper we present an implementation of the Smith-Waterman algorithm. The implementation is done in OpenCL and targets high-end GPUs. This implementation is capable of computing similarity indexes between reference and query sequences. The implementation is designed for the sequence alignment paths calculation. In addition, it is capable of handling very long reference sequences […]
Edgardo Mejia-Roa, Daniel Tabas-Madrid, Javier Setoain, Carlos Garcia, Francisco Tirado, Alberto Pascual-Montano
BACKGROUND: In the last few years, the Non-negative Matrix Factorization (NMF) technique has gained a great interest among the Bioinformatics community, since it is able to extract interpretable parts from high-dimensional datasets. However, the computing time required to process large data matrices may become impractical, even for a parallel application running on a multiprocessors cluster. […]
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