- 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
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
- 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
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
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.