A robust peak detection method for RNA structure inference by high-throughput contact mapping.

MOTIVATION: For high-throughput prediction of the helical arrangements of large RNA molecules, an innovative method termed multiplexed hydroxyl radical (*OH) cleavage analysis (MOHCA) has been proposed. A key step in this promising technique is to detect peaks accurately from noisy radioactivity profiles. Since manual peak finding is laborious and prone to error, an automated peak detection method to improve the accuracy and throughput of MOHCA is required. Existing methods were not applicable to MOHCA due to their high false positive rates. RESULTS: We developed a two-step computational method that can detect peaks from MOHCA profiles in a robust manner. The first step exploits an ensemble of linear and non-linear signal processing techniques to find true peak candidates. In the second step, a binary classifier trained with the characteristics of true and false peaks is used to eliminate false peaks out of the peak candidates. We tested the proposed approach with 2002 MOHCA cleavage profiles and obtained the median recall, precision and F-measure values of 0.917, 0.750 and 0.830, respectively. Compared with the alternatives considered, the proposed method was able to handle false peaks substantially better, thus resulting in 51.0-71.8% higher median values of precision and F-measure. AVAILABILITY: The software and supplementary data are available at http://dna.korea.ac.kr/pub/mohca.

In-DRAM Cache Management for Low Latency and Low Power 3D-Stacked DRAMs.

Recently, 3D-stacked dynamic random access memory (DRAM) has become a promising solution for ultra-high capacity and high-bandwidth memory implementations. However, it also suffers from memory wall problems due to long latency, such as with typical 2D-DRAMs. Although there are various cache management techniques and latency hiding schemes to reduce DRAM access time, in a high-performance system using high-capacity 3D-stacked DRAM, it is ultimately essential to reduce the latency of the DRAM itself. To solve this problem, various asymmetric in-DRAM cache structures have recently been proposed, which are more attractive for high-capacity DRAMs because they can be implemented at a lower cost in 3D-stacked DRAMs. However, most research mainly focuses on the architecture of the in-DRAM cache itself and does not pay much attention to proper management methods. In this paper, we propose two new management algorithms for the in-DRAM caches to achieve a low-latency and low-power 3D-stacked DRAM device. Through the computing system simulation, we demonstrate the improvement of energy delay product up to 67%.

Clustering protein environments for function prediction: finding PROSITE motifs in 3D.

BACKGROUND: Structural genomics initiatives are producing increasing numbers of three-dimensional (3D) structures for which there is little functional information. Structure-based annotation of molecular function is therefore becoming critical. We previously presented FEATURE, a method for describing microenvironments around functional sites in proteins. However, FEATURE uses supervised machine learning and so is limited to building models for sites of known importance and location. We hypothesized that there are a large number of sites in proteins that are associated with function that have not yet been recognized. Toward that end, we have developed a method for clustering protein microenvironments in order to evaluate the potential for discovering novel sites that have not been previously identified. RESULTS: We have prototyped a computational method for rapid clustering of millions of microenvironments in order to discover residues whose surrounding environments are similar and which may therefore share a functional or structural role. We clustered nearly 2,000,000 environments from 9,600 protein chains and defined 4,550 clusters. As a preliminary validation, we asked whether known 3D environments associated with PROSITE motifs were "rediscovered". We found examples of clusters highly enriched for residues that share PROSITE sequence motifs. CONCLUSION: Our results demonstrate that we can cluster protein environments successfully using a simplified representation and K-means clustering algorithm. The rediscovery of known 3D motifs allows us to calibrate the size and intercluster distances that characterize useful clusters. This information will then allow us to find new clusters with similar characteristics that represent novel structural or functional sites.

GPU-based acceleration of an RNA tertiary structure prediction algorithm.

Experimental techniques such as X-ray crystallography and nuclear magnetic resonance have been useful for the accurate determination of RNA tertiary structures. However, high-throughput structure determination using such methods often becomes difficult, due to the need for a large quantity of pure samples. Computational techniques for the prediction of RNA tertiary structures are thus becoming increasingly popular. Most of the existing prediction algorithms are computationally intensive, and there is a clear need for acceleration. In this paper, we propose a parallelization methodology for the fragment assembly of RNA (FARNA) algorithm, one of the most effective methods for computational prediction of RNA tertiary structure. The proposed parallelization scheme exploits multi-core CPUs and GPUs in harmony to maximize their utilization. We tested our approach with a number of RNA sequences and confirmed that it allows the time required for structure prediction to be significantly reduced. With respect to the baseline architecture equipped with a single CPU core, we achieved a speedup of up to approximately 24×(roughly 4× by multi-core CPUs and 20× by GPUs). Compared with a quad-core CPU setup, the proposed approach delivers an additional 12× speedup by utilizing GPU devices. Given that most PCs these days have a multi-core CPU and a GPU card, our methodology will be very helpful for accelerating algorithms in a cost-effective manner.