Thomas C. Carroll, Jude-Thaddeus Ojiaku, Prudence W.H. Wong
In this paper we consider the pair-wise sequence alignment problem with gaps, which is motivated by the resequencing problem that requires to assemble short reads sequences into a genome sequence by referring to a reference sequence. The problem has been studied before for single gap and bounded number of gaps. For single gap, there was […]
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Lev E. Givon, Aurel A. Lazar
We have developed an open software platform called Neurokernel for collaborative development of comprehensive models of the brain of the fruit fly Drosophila melanogaster and their execution and testing on multiple Graphics Processing Units (GPUs). Neurokernel provides a programming model that capitalizes upon the structural organization of the fly brain into a fixed number of […]
Hamed Khakzad, Yasaman Karami, Seyed Shahriar Arab
Protein tertiary structure prediction (PSP) is one of the most challenging problems in bioinformatics. Different methods have been introduced to solve this problem so far, but PSP is computationally intensive and belongs to the NP-hard class. One of the best solutions to accelerate PSP is the use of a massively parallel processing architecture, such graphical […]
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Charalampos S. Kouzinopoulos, Panagiotis D. Michailidis, Konstantinos G. Margaritis
Multiple pattern matching algorithms are used to locate the occurrences of patterns from a finite pattern set in a large input string. Aho-Corasick, Set Horspool, Set Backward Oracle Matching, Wu-Manber and SOG, five of the most well known algorithms for multiple matching require an increased computing power, particularly in cases where large-size datasets must be […]
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Alexander Ross Mace
Acentrosomal microtubules are not bound to a microtubule organising centre yet are still able to form ordered arrays. Two clear examples of this behaviour are the acentrosomal apico-basal (side wall) array in epithelial cells and the parallel organisation of plant cortical microtubules. This research investigates their formation through mathematical modelling and Monte Carlo simulations with […]
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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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