April 2002 - March 2007
Laboratory of Biostatistics
Professor: Katsuhisa Horimoto
Project Research Associate: Sachiyo Aburatani
Project Lecturer: Rui Yamaguchi
Project Research Associate: Atsushi Doi
April 2011 - March 2014
Division of Interactome Medical Sciences
Project Associate Professor: Etsuko Miyamoto-Sato
April 2000 - March 2012
Laboratory of Functional Genomics
Associate Professor: Masao Nagasaki
April 2007 - March 2012
Division of Systems Biomedical Technology
Project Associate Professor: Noriko Goto
Division of Social Communication System for Advanced Clinical Research
Project Professor: Masahiro Kami
- March 2020
Laboratory of DNA Information Analysis
Professor: Satoru MIyano
Out of service databases
Thank you very much for using our service.
JSNP database is a collection of approximately 200,000 gene-based SNP information that includes their location, methods to genotype them, their allele frequencies in Japanese general population. This project was one of the Prime Minister's National Millennium Projects in Japan, with the collaboration of Human Genome Center (HGC), Institute of Medical Science (IMS), The University of Tokyo, and Japan Science and Technology Agency (JST).
We continue to provide data on HGC's Anonymous FTP.ftp://ftp.hgc.jp/pub/hgc/db/snp/
The HiGet service provides full text searches on various biological databases including GenBank, RefSeq, UniProt, PDB, PROSITE and OMIM. The field specific search can narrow down the number of entries retrieved to obtain more specific results.
The Macrophage Pathway Knowledgebase (MACPAK) is a computational system which allows biomedical researchers to query and study the dynamic behaviors of macrophage molecular pathways. It integrates the knowledge of 230 reviews that were carefully checked by specialists for their accuracy and then converted to 230 dynamic mathematical pathway models. MACPAK comprises a total of 24,009 entities and 12,774 processes and is described in the Cell System Markup Language (CSML), an XML format that runs on the Cell Illustrator platform and can be visualized with a customized Cytoscape for further analysis.
CGED (Cancer Gene Expression Database) is a database of gene expression profile and accompanying clinical information. This database offers graphical presentation of expression and clinical data with similarity search and sorting functions.
Out of service software and analysis tools
Thank you very much for using our service.
Parallel PRRN is a sensitve multiple sequence alignment program originally developed by O. Goto (CBRC, AIST) as prrp/prrn. This version was implemented by Y. Totoki (GSC, RIKEN) to run on a SGI machine in parallel. Its algorithm is the best-first search iterative refinement strategy with tree-dependent partitioning. According to an objective test by a third party, it is one of the most sensitive multiple alignment programs in the world (Thompson et al., 1999).
PACADE is a deductive database system which searches for protein substructures similar to a given substructure represented as a series of secondary structures. Linked with other systems, PACADE can visualize query and answer substructures. In addition, it can discover features common and specific to the proteins with similar substructures.
Whoin, which is constructed for Genome-hiroba in 2003, is the one of tools to introduce genome science. It just finds query words in human protein sequences.
XiP (eXtensible integrative Pipeline) is a flexible, editable and modular environment with a user-friendly interface that does not require previous advanced programming skills to run, construct and edit workflows. XiP allows the construction of workflows by linking components written in both R and Java, the analysis of high-throughput data in grid engine systems and also the development of customized pipelines that can be encapsulated in a package and distributed.XiP already comes with several ready-to-use pipeline flows for the most common genomic and transcriptomic analysis and ∼300 computational components. In the latest XiP 3.0, several components run on K computer environment.
An international project to uncover the full picture of the human gene
What is the Human Genome Project?
The genome is the blueprint for life
A genome is the blueprint for life, and one genome corresponds to the genetic information that is passed from parent to child in sperm/eggs.
The body of the genome is a string-like substance called DNA, which consists of four types of bases (letters): A (adenine), G (guanine), T (thymine), and C (cytosine).
The way these four letters are arranged determines how all life works.
The human genome is made up of 3 billion letters. It is believed that there are 20,000 to 30,000 genes in human genomic DNA that work directly.
The Human Genome Project is a Challenge for Humanity
The Human Genome Project will read the entire human DNA sequence (3 billion characters) and elucidate its function.
This grand analysis project has been carried out with international cooperation.
A summary sequence of the total human DNA sequence was determined in 2001, and the total nucleotide sequence was determined in 2003. In addition, in connection with the Human Genome Project, the genomes of various organisms are being analyzed, and the DNA sequences of yeast, E. coli, nematodes, and Drosophila have already been read.
Currently, the HapMap Project, a five-country international collaboration, is underway to create a chromosome-wide protype covering all chromosomes.