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Hamada M.,Mizuho Information and Research Institute | Hamada M.,Japan National Institute of Advanced Industrial Science and Technology | Sato K.,University of Tokyo | Asai K.,Japan National Institute of Advanced Industrial Science and Technology | Asai K.,University of Tokyo
Nucleic Acids Research | Year: 2011

Considerable attention has been focused on predicting the secondary structure for aligned RNA sequences since it is useful not only for improving the limiting accuracy of conventional secondary structure prediction but also for finding non-coding RNAs in genomic sequences. Although there exist many algorithms of predicting secondary structure for aligned RNA sequences, further improvement of the accuracy is still awaited. In this article, toward improving the accuracy, a theoretical classification of state-of-the-art algorithms of predicting secondary structure for aligned RNA sequences is presented. The classification is based on the viewpoint of maximum expected accuracy (MEA), which has been successfully applied in various problems in bioinformatics. The classification reveals several disadvantages of the current algorithms but we propose an improvement of a previously introduced algorithm (CentroidAlifold). Finally, computational experiments strongly support the theoretical classification and indicate that the improved CentroidAlifold substantially outperforms other algorithms. © 2010 The Author(s).

Tanaka S.,Kobe University | Mochizuki Y.,Rikkyo University | Mochizuki Y.,University of Tokyo | Komeiji Y.,Japan National Institute of Advanced Industrial Science and Technology | And 3 more authors.
Physical Chemistry Chemical Physics | Year: 2014

Recent developments in the fragment molecular orbital (FMO) method for theoretical formulation, implementation, and application to nano and biomolecular systems are reviewed. The FMO method has enabled ab initio quantum-mechanical calculations for large molecular systems such as protein-ligand complexes at a reasonable computational cost in a parallelized way. There have been a wealth of application outcomes from the FMO method in the fields of biochemistry, medicinal chemistry and nanotechnology, in which the electron correlation effects play vital roles. With the aid of the advances in high-performance computing, the FMO method promises larger, faster, and more accurate simulations of biomolecular and related systems, including the descriptions of dynamical behaviors in solvent environments. The current status and future prospects of the FMO scheme are addressed in these contexts. This journal is © the Partner Organisations 2014.

Arai E.,National Cancer Center Research Institute | Chiku S.,Mizuho Information and Research Institute | Mori T.,National Cancer Center Research Institute | Gotoh M.,National Cancer Center Research Institute | And 3 more authors.
Carcinogenesis | Year: 2012

To clarify the significance of DNA methylation alterations during renal carcinogenesis, methylome analysis using single-CpG-resolution Infinium array was performed on 29 normal renal cortex tissue (C) samples, 107 non-cancerous renal cortex tissue (N) samples obtained from patients with clear cell renal cell carcinomas (RCCs) and 109 tumorous tissue (T) samples. DNA methylation levels at 4830 CpG sites were already altered in N samples compared with C samples. Unsupervised hierarchical clustering analysis based on DNA methylation levels at the 801 CpG sites, where DNA methylation alterations had occurred in N samples and were inherited by and strengthened in T samples, clustered clear cell RCCs into Cluster A (n = 90) and Cluster B (n = 14). Clinicopathologically aggressive tumors were accumulated in Cluster B, and the cancer-free and overall survival rates of patients in this cluster were significantly lower than those of patients in Cluster A. Clear cell RCCs in Cluster B were characterized by accumulation of DNA hypermethylation on CpG islands and considered to be CpG island methylator phenotype (CIMP)-positive cancers. DNA hypermethylation of the CpG sites on the FAM150A, GRM6, ZNF540, ZFP42, ZNF154, RIMS4, PCDHAC1, KHDRBS2, ASCL2, KCNQ1, PRAC, WNT3A, TRH, FAM78A, ZNF671, SLC13A5 and NKX6-2 genes became hallmarks of CIMP in RCCs. On the other hand, Cluster A was characterized by genome-wide DNA hypomethylation. These data indicated that DNA methylation alterations at precancerous stages may determine tumor aggressiveness and patient outcome. Accumulation of DNA hypermethylation on CpG islands and genome-wide DNA hypomethylation may each underlie distinct pathways of renal carcinogenesis. Abbreviations: BAMCAbacterial artificial chromosome array-based methylated CpG island amplification. Cnormal renal cortex tissue obtained from patients without any primary renal tumor. CIMPCpG island methylator phenotype. HCChepatocellular carcinoma. Nnon-cancerous renal cortex tissue obtained from patients with clear cell renal cell carcinomas. NCBINational Center for Biotechnology Information. RCCrenal cell carcinoma. Ttumorous tissue. TNMTumor-Node-Metastasis. © The Author 2012. Published by Oxford University Press. All rights reserved.

Frith M.C.,Tokyo Institute of Technology | Hamada M.,Tokyo Institute of Technology | Hamada M.,Mizuho Information and Research Institute | Horton P.,Tokyo Institute of Technology
BMC Bioinformatics | Year: 2010

Background: Genome sequence alignments form the basis of much research. Genome alignment depends on various mundane but critical choices, such as how to mask repeats and which score parameters to use. Surprisingly, there has been no large-scale assessment of these choices using real genomic data. Moreover, rigorous procedures to control the rate of spurious alignment have not been employed.Results: We have assessed 495 combinations of score parameters for alignment of animal, plant, and fungal genomes. As our gold-standard of accuracy, we used genome alignments implied by multiple alignments of proteins and of structural RNAs. We found the HOXD scoring schemes underlying alignments in the UCSC genome database to be far from optimal, and suggest better parameters. Higher values of the X-drop parameter are not always better. E-values accurately indicate the rate of spurious alignment, but only if tandem repeats are masked in a non-standard way. Finally, we show that γ-centroid (probabilistic) alignment can find highly reliable subsets of aligned bases.Conclusions: These results enable more accurate genome alignment, with reliability measures for local alignments and for individual aligned bases. This study was made possible by our new software, LAST, which can align vertebrate genomes in a few hours http://last.cbrc.jp/. © 2010 Frith et al; licensee BioMed Central Ltd.

Mizuho Information and Research Institute | Date: 2012-08-07

In the present invention, a control section of a CRM server performs editing processing for TPO (the time, the place, and the occasion) requirements. Next, a control section of a TPO server registers the TPO requirements in order to convert the same to TPO definitions. Then, the control section performs setting processing for the TPO definitions. A portable terminal identifies the current location and the current time. Then, a control section verifies TPO definition state transitioning. If transitioning of the TPO definition state is detected, the control section performs TPO definition state transition notification processing. The control section of the portable terminal performs individual control processing on the basis of the TPO definitions.

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