22/5/2006Announcement of a new book by Imperial College Press:
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LARGE-SCALE GENOME SEQUENCE PROCESSING
by Masahiro Kasahara & Shinichi Morishita (University of Tokyo, Japan)
Efficient computer programs have made it possible to elucidate and analyze large-scale genomic sequences. Fundamental tasks, such as the assembly of numerous whole-genome shotgun fragments, the alignment of complementary DNA sequences with a long genome, and the design of gene-specific primers or oligomers, require efficient algorithms and state-of-the-art implementation techniques. This textbook emphasizes basic software implementation techniques for processing large-scale genome sequences and provides executable sample programs.
Supplementary Programs |
11/5/2006 We have released a web service to design multiplex genomic PCR primer for the human genome.
Tomoyuki Yamada, Haruhiko Souma, Shinichi Morishita.
PrimerStation: a highly specific multiplex genomic PCR primer design server for the human genome.
Nucl. Acids Res. 2006 34: W665-W669; doi:10.1093/nar/gkl297
Web Site: http://ps.cb.k.u-tokyo.ac.jp/
19/1/2006 Saccharomyces Cerevisiae Morphological Data Analysis
Publication
Yoshikazu Ohya, Jun Sese(*), Masashi Yukawa(*), Fumi Sano, Yoichiro Nakatani, Taro L. Saito, Ayaka Saka, Tomoyuki Fukuda, Satoru Ishihara, Satomi Oka, Genjiro Suzuki, Machika Watanabe, Aiko Hirata, Miwaka Ohtani, Hiroshi Sawai, Nicolas Fraysse, Jean-Paul Latge, Jean M. Francois, Markus Aebi, Seiji Tanaka, Sachiko Muramatsu, Hiroyuki Araki, Kintake Sonoike, Satoru Nogami, and Shinichi Morishita.
High-dimensional and large-scale phenotyping of yeast mutants Proc Natl Acad Sci U S A. 2005 Dec 27;102(52):19015-20.(* equally contributed authors)
See also Nature Review — Research Highlights
Patrick Goymer: Shaping up the genome. Nature Review, Vol.7, Feb. 2006; 79
18/1/2006 Chimpanzee and human Y chromosomes
Publication
Yoko Kuroki, Atsushi Toyoda, Hideki Noguchi, Todd D Taylor, Takehiko Itoh, Dae-Soo Kim, Dae-Won Kim, Sang-Haeng Choi, Il-Chul Kim, Han Ho Choi, Yong Sung Kim, Yoko Satta, Naruya Saitou, Tomoyuki Yamada, Shinichi Morishita, Masahira Hattori, Yoshiyuki Sakaki, Hong-Seog Park and Asao Fujiyama
Comparative analysis of chimpanzee and human Y chromosomes unveils complex evolutionary pathway.
Nat Genet. 2006 Jan 1; [Epub ahead of print]
12/9/2005 The latest assembly revision 200506 of the Medaka genome and its annotation are now available in the UT Genome Browser (Medaka).
1/9/2005 siDirect and dsCheck are updated.
New version of siDirect provides a function of designing siRNA sequeces for genes of rat, chicken, and dog. dsCheck, sensitive off-target search website for dsRNA-mediated RNAi , is also able to process requests on Drosophila melanogaster, C. elegans, Arabidopsis thaliana, and rice.
7/4/2005 The following servers have been empowered with novel functions:
SCMD： Data mining functions of predicting functions og genes using 500 quantitative morphological parameters.
Taro L. Saito (*), Jun Sese (*), Yoichiro Nakatani, Fumi Sano, Masashi Yukawa, Yoshikazu Ohya, and Shinichi Morishita
Data Mining Tools for the Saccharomyces cerevisiae Morphological Database.
Nucleic Acids Research 2005 33(Web Server issue):W589-W591 * indicates the joint first authors.
dsCheck: The software performs highly sensitive off-target search for dsRNA-mediated RNA interfence.
Yuki Naito (*), Tomoyuki Yamada (*), Takahiro Matsumiya, Kumiko Ui-Tei, Kaoru Saigo, and Shinichi Morishita
dsCheck: highly sensitive off-target search software for dsRNA-mediated RNA interference.
Nucleic Acids Research 2005 33(Web Server issue):W753-W757 * indicates the joint first authors.
17/12/2004.The following two papers are available in Bioinformatics journal web site.
Tomoyuki Yamada and Shinichi Morishita. Accelerated off-target search algorithm for siRNA.
Bioinformatics, Advance Access published on December 14, 2004; doi: 10.1093/bioinformatics/bti155.
Jun Sese, Yukinori Kurokawa, Morito Monden, Kikuya Kato and Shinichi Morishita.
Constrained Clusters of Gene Expression Profiles with Pathological Features,
Bioinformatics, 20: 3137 – 3145, 2004.
01/09/2004 The following two papers were published.
Shin-ichi Hashimoto, Yutaka Suzuki, Yasuhiro Kasai, Kei Morohoshi, Tomoyuki Yamada, Jun Sese, Shinichi Morishita, Sumio Sugano, Kouji Matsushima. 5′-end SAGE for the analysis of transcriptional start sites.
Nature Biotechnology 22, 1146 – 1149, 2004. Go to 5′SAGE web server site
Masaya Suzuki, Ryoji Igarashi, Mizuho Sekiya, Takahiko Utsugi, Shinichi Morishita, Masashi Yukawa, Yoshikazu Ohya.
Dynactin is involved in a checkpoint to monitor cell wall synthesis in Saccharomyces cerevisiae.
Nature Cell Biology 6, 861 – 871, 2004.
17/08/2004 The UT Genome Browser for Medaka fish is now open to the public.
13/08/2004 Our following paper is honored with one of top papers in Volume 32, Web Server Issue, Nucleic Acids Research.
Yuki Naito(*), Tomoyuki Yamada(*), Kumiko Ui-Tei, Shinichi Morishita, and Kaoru Saigo.
siDirect: highly effective, target-specific siRNA design software for mammalian RNA interference.
Nucl. Acids Res. 2004 32: W124-129. * indicates the joint first authors.
Information (cached)
09/08/2004 The web database 5′SAGE (5′-end Serial Analysis of Gene Expression database) is publicized.
