Che-Lun Hun, Guan-Jie Hua
With the rapid growth of next generation sequencing technologies, such as Slex, more and more data have been discovered and published. To analysis such huge data the computational performance is an important issue. Recently, many tools, such as SOAP, have been implemented on Hadoop and GPU parallel computing architectures. BLASTP is an important tool, implemented […]
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Andrew L. Beam, Alison Motsinger-Reif, Jon Doyle
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. A non-parametric Bayesian approach in the form of a Bayesian neural network is proposed for use in analyzing genetic association […]
Yukun Zhong, ZhiWei He, XianHong Wang, Liao Gang
With early hardware limitations of the GPU (lack of synchronization primitives and limited memory caching mechanisms)can make GPU-based computation inefficient, and emerging DNA sequence technologies open up more opportunities for molecular biology. This paper presents the issues of parallel implementation of longest overlap region Problem on a multiprocessor GPU using the Compute Unified Device Architecture […]
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Yukun Zhong, ZhiWei He, XianHong Wang, XiongBin Cao
Traditionally, we usually utilize the method of shotgun to cut a DNA sequence into pieces and we have to reconstruct the original DNA sequence from the pieces, those are widely used method for DNA assembly. Emerging DNA sequence technologies open up more opportunities for molecular biology. This paper introduce a new method to improve the […]
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Neri Mickael, Denis Mestivier
MOTIVATION: The Stochastic Simulation Algorithm (SSA) has largely diffused in the field of systems biology. This approach needs many realizations for establishing statistical results on the system under study. It is very computationnally demanding, and with the advent of large models this burden is increasing. Hence parallel implementation of SSA are needed to address these […]
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J. Li, S. Ranka, S. Sahni
We develop cache efficient, multicore, and GPU algorithms for RNA folding using Nussinov’s equations. Our cache efficient algorithm provides a speedup between 1.6 and 3.0 relative to a naive straightforward single core code. The multicore version of the cache efficient single core algorithm provides a speedup, relative to the naive single core algorithm, between 7.5 […]
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S. Stella, R. Chignola, E. Milotti
We have developed a numerical model that simulates the growth of small avascular solid tumors. At its core lies a set of partial differential equations that describe diffusion processes as well as transport and reaction mechanisms of a selected number of nutrients. Although the model relies on a restricted subset of molecular pathways, it compares […]
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Usman Roshan
Exact short read mapping to whole genomes with the Smith-Waterman algorithm is computationally expensive yet highly accurate when aligning reads with mismatches and gaps. We introduce a GPU program called MaxSSmap with the aim of achieving comparable accuracy to Smith-Waterman but with faster runtimes. Similar to mainstream approaches MaxSSmap identifies a local region of the […]
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Gustavo Encarnacao
Since the discovery of Deoxyribonucleic Acid (DNA) significant technological advances were made, leading to very large amounts of data gathered for analysis. The tools for this analysis however have advanced at a slower pace and have become one of the limiting factors of new discoveries in this field of research. Recently, from the 3D game […]
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H. Khaled, R. El Gohary, N.L. Badr, H. M. Faheem
This paper provides a novel framework for accelerating the solution of the pairwise DNA sequence alignment problem using CUDA parallel paradigm available on the NVIDIA GPU. The main idea is to implement a new algorithm that assigns different nucleotide weights using GPU architectures then merge the subsequences of match using CPU to get the optimum […]
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Adam Gudys, Sebastian Deorowicz
Multiple sequence alignment is a crucial task in a number of biological analyses like secondary structure prediction, domain searching, phylogeny, etc. MSAProbs is currently the most accurate alignment algorithm, but its effectiveness is obtained at the expense of computational time. In the paper we present QuickProbs, the variant of MSAProbs customised for graphics processors. We […]
Aleksandr Drozd, Naoya Maruyama, Satoshi Matsuoka
This paper describes a performance model for read alignment problem, one of the most computationally intensive tasks in bioinformatics. We adapted Burrows Wheeler transform based index to be used with GPUs to reduce overall memory footprint. A mathematical model of computation and communication costs was developed to find optimal memory partitioning for index and queries. […]
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