J. Li, S. Ranka, S. Sahni
We develop novel single-GPU parallelizations of the Smith-Waterman algorithm for pairwise sequence alignment. Our algorithms, which are suitable for the alignment of a single pair of very long sequences, can be used to determine the alignment score as well as the actual alignment. Experimental results demonstrate an order of magnitude reduction in run time relative […]
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R.P. Souto, C. Osthoff, A.T.R. de Vasconcelos, D.A. Augusto, P.L. da Silva Dias, A. Rodriguez, O. Trelles, M. Ujaldon
High-density oligonucleotide microarrays allow several millions of genetic markers in a single experiment to be observed. Current bioinformatics tools for gene expression quantile data normalization are unable to process such huge data sets. In parallel with this reality, the huge volume of molecular data produced by current high-throughput technologies in modern molecular biology has increased […]
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Guillaume Chapuis
The exponential growth in bioinformatics data generation and the stagnation of processor frequencies in modern processors stress the need for efficient implementations that fully exploit the parallel capabilities offered by modern computers. This thesis focuses on parallel algorithms and implementations for bioinformatics problems. Various types of parallelism are described and exploited. This thesis presents applications […]
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Sungin Park, Soo-Yong Shin, Kyu-Baek Hwang
BACKGROUND: Multidimensional scaling (MDS) is a widely used approach to dimensionality reduction. It has been applied to feature selection and visualization in various areas. Among diverse MDS methods, the classical MDS is a simple and theoretically sound solution for projecting data objects onto a low dimensional space while preserving the original distances among them as […]
Syed Faraz Mahmood
Advances in sequencing technologies have revolutionized the field of genomics by providing cost effective and high throughput solutions. In this paper, we develop a parallel sequence assembler implemented on general purpose graphic processor units (GPUs). Our work was largely motivated by a growing need in the genomic community for sequence assemblers and increasing use of […]
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Tony Kam-Thong
Recent advances in sequencing technology and automated phenotyping render it possible to study the relationship between genotype and phenotype at an unprecedented level of detail. While mapping phenotypes to single loci in the genome is a standard technique in Statistical Genetics, the problem of epistasis search, that is mapping phenotypes to pairs of loci, remains […]
Jiadong Wu, Bo Hong, Takako Takeda, Jun-tao Guo
BACKGROUND: Protein-DNA docking is a very challenging problem in structural bioinformatics and has important implications in a number of applications, such as structure-based prediction of transcription factor binding sites and rational drug design. Protein-DNA docking is very computational demanding due to the high cost of energy calculation and the statistical nature of conformational sampling algorithms. […]
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David Seide
This project focuses on using GPGPUs for solving the inexact alignment of short-reads with respect to a reference indexed using the Burrows-Wheeler Transform. To be more specific we dealt with a solution of an alignment that allows up to one error.
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Pooya Zandevakili, Ming Hu, Zhaohui Qin
Computational detection of TF binding patterns has become an indispensable tool in functional genomics research. With the rapid advance of new sequencing technologies, large amounts of protein-DNA interaction data have been produced. Analyzing this data can provide substantial insight into the mechanisms of transcriptional regulation. However, the massive amount of sequence data presents daunting challenges. […]
Sylvain Robert Rivard, Jean-Gabriel Mailloux, Rachid Beguenane, Hung Tien Bui,
BACKGROUND: This paper proposes a method of implementing parallel gene prediction algorithms in MATLAB. The proposed designs are based on either Goertzel’s algorithm or on FFTs and have been implemented using varying amounts of parallelism on a central processing unit (CPU) and on a graphics processing unit (GPU). FINDINGS: Results show that an implementation using […]
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Peng Jia, Liming Xuan, Lei Liu, Chaochun Wei
Metagenomic sequence classification is a procedure to assign sequences to their source genomes. It is one of the important steps for metagenomic sequence data analysis. Although many methods exist, classification of high-throughput metagenomic sequence data in a limited time is still a challenge. We present here an ultra-fast metagenomic sequence classification system (MetaBinG) using graphic […]
Wuchao Situ, Yau-King Lam, Yi Xiao, P.W.M. Tsang, Chi-Sing Leung
In this paper, a novel GPU accelerated scheme for the PK-means gene clustering algorithm is proposed. According to the native particle-pair structure of the PKmeans algorithm, a fragment shader program is tailor-made to process a pair of particles in one pass for the computationintensive portion. As the output channel of a fragment consisting of 4 […]
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Free GPU computing nodes at hgpu.org

Registered users can now run their OpenCL application at hgpu.org. We provide 1 minute of computer time per each run on two nodes with two AMD and one nVidia graphics processing units, correspondingly. There are no restrictions on the number of starts.

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Node 1
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  • RAM: 16GB
  • OS: OpenSUSE 12.2
  • SDK: nVidia CUDA Toolkit 5.0.35, AMD APP SDK 2.8

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