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Paolo Cazzaniga, Marco S. Nobile, Daniela Besozzi, Matteo Bellini, Giancarlo Mauri
The introduction of general-purpose Graphics Processing Units (GPUs) is boosting scientific applications in Bioinformatics, Systems Biology and Computational Biology. In these fields, the use of high-performance computing solutions is motivated by the need of performing large numbers of in silico analysis to study the behavior of biological systems in different conditions, which necessitate a computing […]
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Sampath Kumar, P. K. Baruah
GPU parallelism for real applications can achieve enormous performance gain. CPU-GPU Communication is one of the major bottlenecks that limit this performance gain. Among several libraries developed so far to optimize this communication, DyManD (Dynamically Managed Data) provides better communication optimization strategies and achieves better performance on a single GPU. Smith-Waterman is a well known […]
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Da Li, Kittisak Sajjapongse, Huan Truong, Gavin Conant, Michela Becchi
Several problems in computational biology require the all-against-all pairwise comparisons of tens of thousands of individual biological sequences. Each such comparison can be performed with the well-known Needleman-Wunsch alignment algorithm. However, with the rapid growth of biological databases, performing all possible comparisons with this algorithm in serial becomes extremely time-consuming. The massive computational power of […]
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Lucas Beyer, Paolo Bientinesi
In the context of the genome-wide association studies (GWAS), one has to solve long sequences of generalized least-squares problems; such a task has two limiting factors: execution time often in the range of days or weeks and data management data sets in the order of Terabytes. We present an algorithm that obviates both issues. By […]
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Cheng Ling
Bioinformatics and Computational Biology (BCB) is a relatively new multidisciplinary field which brings together many aspects of the fields of biology, computer science, statistics, and engineering. Bioinformatics extracts useful information from biological data and makes these more intuitive and understandable by applying principles of information sciences, while computational biology harnesses computational approaches and technologies to […]
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Xiaoquan Su, Jian Xu, Kang Ning
BACKGROUND: Metagenomics method directly sequences and analyses genome information from microbial communities. There are usually more than hundreds of genomes from different microbial species in the same community, and the main computational tasks for metagenomic data analyses include taxonomical and functional component examination of all genomes in the microbial community. Metagenomic data analysis is both […]
Lin Ma, Roger D. Chamberlain
Graphics engines are excellent execution platforms for high-throughput computations that exploit a large degree of available parallelism. The achieved performance is, however, highly dependent on the access patterns that the application imposes on the memory subsystem. Here, we propose an analytic model that helps improve the understanding of the performance of memory-limited kernels that employ […]
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Themistoklis K. Pyrgiotis, Charalampos S. Kouzinopoulos, Konstantinos G. Margaritis
One of the most significant issues of the computational biology is the multiple pattern matching for locating nucleotides and amino acid sequence patterns into biological databases. Sequential implementations for these processes have become inadequate, due to an increasing demand for more computational power. Graphic cards offer a high parallelism computational power improving the performance of […]
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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. […]
Ricardo J. Barrientos, Jose I. Gomez, Christian Tenllado, Manuel Prieto Matias, Mauricio Marin
Similarity search has been widely studied in the last years, as it can be applied to several fields such as searching by content in multimedia objects, text retrieval or computational biology. These applications usually work on very large databases that are often indexed off-line to enable the acceleration of online searches. However, to maintain an […]
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Haixiang Shi, Bertil Schmidt, Weiguo Liu, Wolfgang Muller-Wittig
BACKGROUND: Mutual information is a measure of similarity between two variables. It has been widely used in various application domains including computational biology, machine learning, statistics, image processing, and financial computing. Previously used simple histogram based mutual information estimators lack the precision in quality compared to kernel based methods. The recently introduced B-spline function based […]
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 […]
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