著者

MASAHITO OHUE YURI MATSUZAKI YUTAKA AKIYAMA

出版者

Japanese Society for Bioinformatics

雑誌

Genome Informatics (ISSN:09199454)

巻号頁・発行日

vol.25, no.1, pp.25-39, 2011 (Released:2011-08-03)

参考文献数

22

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Elucidating protein-RNA interactions (PRIs) is important for understanding many cellular systems. We developed a PRI prediction method by using a rigid-body protein-RNA docking calculation with tertiary structure data. We evaluated this method by using 78 protein-RNA complex structures from the Protein Data Bank. We predicted the interactions for pairs in 78×78 combinations. Of these, 78 original complexes were defined as positive pairs, and the other 6,006 complexes were defined as negative pairs; then an F-measure value of 0.465 was obtained with our prediction system.

著者

Hisahiko Sato Takashi Yoshioka Akihiko Konagaya Tetsuro Toyoda

出版者

Japanese Society for Bioinformatics

雑誌

Genome Informatics (ISSN:09199454)

巻号頁・発行日

vol.12, pp.512-514, 2001 (Released:2011-07-11)

参考文献数

5

著者

Myungguen Chung Kiho Park In Song Koh Jong Park

出版者

日本バイオインフォマティクス学会

雑誌

Genome Informatics (ISSN:09199454)

巻号頁・発行日

vol.12, pp.478-479, 2001 (Released:2011-07-11)

参考文献数

2

著者

LESLEY J COLLINS PATRICK J BIGGS CLAUDIA VOELCKEL SIMON JOLY

出版者

日本バイオインフォマティクス学会

雑誌

Genome Informatics (ISSN:09199454)

巻号頁・発行日

vol.21, pp.3-14, 2008 (Released:2011-07-11)

参考文献数

10

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Transcriptome analysis using high-throughput short-read sequencing technology is straightforward when the sequenced genome is the same species or extremely similar to the reference genome. We present an analysis approach for when the sequenced organism does not have an already sequenced genome that can be used for a reference, as will be the case of many non-model organisms. As proof of concept, data from Solexa sequencing of the polyploid plant Pachycladon enysii was analysed using our approach with its nearest model reference genome being the diploid plant Arabidopsis thaliana. By using a combination of mapping and de novo assembly tools we could determine duplicate genes belonging to one or other of the genome copies. Our approach demonstrates that transcriptome analysis using high-throughput short-read sequencing need not be restricted to the genomes of model organisms.

著者

伊奈 康夫 五條堀 孝

出版者

Japanese Society for Bioinformatics

雑誌

Genome Informatics (ISSN:09199454)

巻号頁・発行日

vol.2, pp.74-77, 1991

著者

Hirotugu Akaike

出版者

Japanese Society for Bioinformatics

雑誌

Genome Informatics (ISSN:09199454)

巻号頁・発行日

vol.14, pp.263-265, 2003 (Released:2011-07-11)

参考文献数

4

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The role of a model is to provide adequate knowledge to handle a particular problem. The work of modeling starts on the basis of the feel and knowledge of the object and proceeds by developing guesses about the structure of the object. In this paper characteristics of this process are demonstrated with the example of the analysis of the golf swing motion.

著者

Yoshihiro Yamanishi Masumi Itoh Minoru Kanehisa

出版者

Japanese Society for Bioinformatics

雑誌

Genome Informatics (ISSN:09199454)

巻号頁・発行日

vol.13, pp.61-70, 2002 (Released:2011-07-11)

参考文献数

12

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In recent years, the analysis of orthologous genes based on phylogenetic profiles has received popularity in bioinfomatics. We propose a new method to extract organism groups and their hierarchy from phylogenetic profiles using the independent component analysis (ICA). The method involves first finding independent axes in the projected space from the multivariate data matrix representing phylogenetic profiles for a number of orthologous genes. Then the extracted axes are correlated with major organism groups, according to the extent of affiliaion of axes scores for all the genes to specific organisms. The ICA was applied to the phylogenetic profiles created for 2875 orthologs in 77 organisms by using the KEGG/GENES database. The 9 extracted components out of 18 predefined components well represented the organism groups as categorized in KEGG. Furthermore, we performed the cluster analysis and obtained the hierarchy of organism groups.

著者

Qian Xie Zoran Obradovic Gregory E. Arnold Ethan Garner Pedro Romero A.Keith Dunker

出版者

Japanese Society for Bioinformatics

雑誌

Genome Informatics (ISSN:09199454)

巻号頁・発行日

vol.9, pp.193-200, 1998 (Released:2011-07-11)

参考文献数

22

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The conditional probability, P (s|x), is a statement of the probability that the event, s, will occur given prior knowledge for the value of x. If x is given and if s is randomly distributed, then an empirical approximation of the true conditional probability can be computed by the application of Bayes' Theorem. Here s represents one of two structural classes, either ordered, so, or disordered, sd, and x represents an attribute value calculated over a window of 21 amino-acids. Plots of P (slx) versus x provide information about the correlation between the given sequence attribute and disorder or order. These conditional probability plots allow quantitative comparisons between individual attributes for their ability to discriminate between order and disorder states. Using such quantitative comparisons, 38 different sequence attributes have been rank-ordered. Attributes based on cysteine, the aromatics, flexible tendencies, and charge were found to be the best attributes for distinguishing order and disorder among those tested so far.

著者

GÜRLER AYSAM KNAPP ERNST-WALTER

出版者

Japanese Society for Bioinformatics

雑誌

Genome Informatics (ISSN:09199454)

巻号頁・発行日

vol.18, pp.183-191, 2007

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We evaluate the performance of common substitution matrices with respect to structural similarities. For this purpose, we apply an all-versus-all pairwise sequence alignment on the ASTRAL40 [7] dataset, consisting of 7290 entries with a pairwise sequence identity of at most 40%. Afterwards, we compare the 100 highest scoring sequence alignments to their corresponding structural alignments, which we obtain from our structure alignment database. Our database consists of about 18.6 million pairwise entries. We calculated these alignments by applying the current version of GANGSTA [1], our non-sequential structural alignment tool, on about 26 million pairs. The results illustrate the difficulty of homology based protein structure prediction in cases of low sequence similarity. Further, the large fraction of structurally similar proteins in the ASTRAL40 dataset is quantitatively measured. Thereby, this investigation yields a new perspective on the topic of sequence and structure relation. Hence, our finding is a large-scale quality measure for any sequence based method, which aims to detect structural similarities.

著者

Akifumi Yamashita Ken Kurokawa Teruo Yasunaga

出版者

日本バイオインフォマティクス学会

雑誌

Genome Informatics (ISSN:09199454)

巻号頁・発行日

vol.14, pp.418-419, 2003 (Released:2011-07-11)

参考文献数

3

著者

Ju-Youn Lee In Song Koh

出版者

日本バイオインフォマティクス学会

雑誌

Genome Informatics (ISSN:09199454)

巻号頁・発行日

vol.12, pp.482-483, 2001 (Released:2011-07-11)

参考文献数

5

著者

Peter J. Waddell Hirohisa Kishino Rissa Ota

出版者

日本バイオインフォマティクス学会

雑誌

Genome Informatics (ISSN:09199454)

巻号頁・発行日

vol.12, pp.141-154, 2001 (Released:2011-07-11)

参考文献数

28

被引用文献数

252

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A major effort is being undertaken to sequence an array of mammalian genomes. Coincidentally, the evolutionary relationships of the 18 presently recognized orders of placental mammals are only just being resolved. In this work we construct and analyse the largest alignments of amino acid sequence data to date. Our findings allow us to set up a series of superordinal groups (clades) to act as prior hypotheses for further testing. Important findings include strong evidence for a clade of Euarchonta+Glires (=Supraprimates) comprised of primates, flying lemurs, tree shrews, lagomorphs and rodents. In addition, there is good evidence for a clade of all placental mammals except Xenarthra and Afrotheria (=Boreotheria) and for the previously recognised clades Laurasiatheria, Scrotifera, Fereuungulata, Ferae, Afrotheria, Euarchonta, Glires, and Eulipotyphla. Accordingly, a revised classification of the placental mammals is put forward. Using this and molecular divergence-time methods, the ages of the superordinal splits are estimated. While results are strongly consistent with the earliest superordinal divergences all being gt; 65 mybp (Cretaceous period), they suffer from greater uncertainty than presently appreciated. The early primate split of tarsiers from the anthropoid lineage at '55 mybp is seen to be an especially informative fossil calibration point. A statistical framework for testing clades using SINE data is presented and reveals significant support for the tarsier/anthropoid clade, as well as the clades Cetruminantia and Whippomorpha. Results also underline our thesis that while sequence analysis can help set up hypothesised clades, SINEs obtainable from sequencing 1-2 MB regions of placental genomes are essential to testing them. In contrast, derivations suggest that empirical Bayesian methods for sequence data may not be robust estimators of clades. Our findings, including the study of genes such as TP53, make a good case for the tree shrew as a closer relative of primates than rodents, while also showing a slower rate of evolution in key cell cycle genes. Tree shrews are consequently high value experimental animals and a strong candidate for a genome sequencing initiative.

著者

Yutaka Ueno Kiyoshi Asai Masanori Arita

出版者

日本バイオインフォマティクス学会

雑誌

Genome Informatics (ISSN:09199454)

巻号頁・発行日

vol.10, pp.166-175, 1999 (Released:2011-07-11)

参考文献数

16

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We have constructed a general framework for integrating application programs with control through a local Web browser. This method is based on a simple inter-process message function from an external process to application programs. Commands to a target program areprepared in a script file, which is parsed by a message dispatcher program. When it is used as ahelper application to a Web browser, these messages will be sent from the browser by clicking a hyper-link in a Web document. Our framework also supports pluggable extension-modules for application programs by means of dynamic linking. A prototype system is implemented on our molecular structure-viewer program, MOSBY. It successfully featured a function to load an extension-module required for the docking study of molecular fragments from a Web page. Our simple framework facilitates the concise configuration of Web softwares without complicated knowledge on network computation and security issues. It is also applicable for a wide range of network computations processing private data using a Web browser.