Archives

Past Information

Closed Laboratories/Divisions

April 2002 - March 2007

Laboratory of Biostatistics

Professor: Katsuhisa Horimoto

Project Research Associate: Sachiyo Aburatani

Project Lecturer: Rui Yamaguchi

Project Research Associate: Atsushi Doi

http://www.bic.kyoto-u.ac.jp/egis/

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

Closed

Division of Social Communication System for Advanced Clinical Research

Project Professor: Masahiro Kami

- March 2020

Laboratory of DNA Information Analysis

Professor: Satoru MIyano

Message from Successive Center Directors

 
 

Out of service databases

Thank you very much for using our service.

JSNP

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/

HiGet

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.

MACPAK

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

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

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

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

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.

Integrated database system of mapping and sequence data.

Software tool to aid contig map construction.

Sequence assembler and editor for the nested deletion sequencing method.

Genome integrated database retrieval environment.

Structure alignment program for 3D protein structures.

Software for image analysis system for 2D gel electrophoresis of genomic DNA.

A protein name annotation tool based on PROPER (PROtein Proper-noun Extraction Rules).

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

 

  1. 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.

  2. 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).

  3. The way these four letters are arranged determines how all life works.

  4. 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

  1. The Human Genome Project will read the entire human DNA sequence (3 billion characters) and elucidate its function.

  2. This grand analysis project has been carried out with international cooperation.

  3. 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.

  4. Currently, the HapMap Project, a five-country international collaboration, is underway to create a chromosome-wide protype covering all chromosomes.​

 
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