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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. […]
Jan Busa Jr., Jan Busa, Shura Hayryan, Chin-Kun Hu, Ming-Chya Wu
Here we present the revised and newly rewritten version of our earlier published CAVE package [J. Busa et al., Comput. Phys. Commun. 181 (2010) 2116] which was originally written in FORTRAN. The package has been rewritten in C language, the algorithm has been parallelized and implemented using OpenCL. This makes the program convenient to run […]
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Benjamin J. Block
A system in a metastable state needs to overcome a certain free energy barrier to form a droplet of the stable phase. Standard treatments assume spherical droplets, but this is not appropriate in the presence of an anisotropy, such as for crystals. The anisotropy of the system has a strong effect on their surface free […]
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Yun Tian, Bojian Xu
Repeat finding in strings has important applications in subfields such as computational biology. The challenge of finding the longest repeats covering particular string positions was recently proposed and solved by Ileri et al., using a total of the optimal O(n) time and space, where n is the string size. However, their solution can only find […]
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Matija Korpar, Martin Sosic, Dino Blazeka, Mile Sikic
The deluge of next-generation sequencing (NGS) data and expanding database poses higher requirements for protein similarity search. State-of-the-art tools such as BLAST are not fast enough to cope with these requirements. Because of that it is necessary to create new algorithms that will be faster while keeping similar sensitivity levels. The majority of protein similarity […]
Andrew L Beam, Alison Motsinger-Reif, Jon Doyle
BACKGROUND: Discovering causal genetic variants from large genetic association studies poses many difficult challenges. Assessing which genetic markers are involved in determining trait status is a computationally demanding task, especially in the presence of gene-gene interactions. RESULTS: A non-parametric Bayesian approach in the form of a Bayesian neural network is proposed for use in analyzing […]
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