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).

>JSNP

The Cell System Markup Language (CSML) is an XML format for modeling, visualizing and simulating biopathways. CSML supports to represent several pathway types including metabolic, signaling, and genetic regulatory pathways. This project aims to facilitate the exchange of biopathway data in different formats. Effort has been made for data conversion from other XML formats. In addition, to allow extensible and flexible features of CSML, the Cell System Ontology (CSO) has been developed.

>CSML/CSO

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.

>HiGet

Database of human transcriptional start sites and full-length cDNAs (Prof. Sugano and Prof. Nakai)

>DBTSS

Database of transcription factors and promoters of Bacillus subtilis from literatures (Prof. Nakai et al.)

>DBTBS

Database of tunicate promoters, transcription factors and conserved regulatory regions.

>DBTGR

Full length cDNA database supported by NEDO (Prof. Sugano's group)

>Full length cDNA

An old collection of aberrant splicing (i.e., abnormal splicing caused mostly by point mutations and revealed as hereditary diseases) by Prof. Nakai (HGC)

>Aberrant Splicing Database

Database of homologous, experimentally determined, protein-protein interactions across 9 species.

>Hintdb

Database of predicted true protein-protein interactions in high-throughput interaction datasets.

>HitPredict

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.

>CGED

The KEGG DAS is a genome browser for all organisms included in the KEGG (Kyoto Encyclopedia of Genes and Genomes) database. The service utilizes the GBrowse as an uniformed user interface and to support DAS (Distributed Annotation System) for the community annotation.

>KEGG DAS

eF-site is a database for molecular surface of proteins along with the electrostatic potential and functional site information. It's named after "electrostatic surface of functional site".

>eF-site

Human genes, proteins, and diseases DB by Weizmann Inst. Sci.

>GeneCards (mirror)

BACE (Bio Association CEntral) aims to work as an association hub of various types of biological information. BACE's associative search provides users with effective way of retrieving related information even from different databases. In other words, BACE dynamically re-organizes the vast information space based on the user's information need.

>BACE

radiation hybrid map of OLETF rat by Otsuka GEN Res. Inst., Otsuka Pharm. Co.,Ltd and others

>Rat Genome Map

Full-malaria is the database of full-length cDNAs of parasites. 5'-end-one-pass sequences of the cDNA libraries produced from the erythrocytic malaria parasites and the tachyzoites of toxoplasma parasites are mapped onto the genome sequences. It also contains 5'-end-one-pass sequences of the cyst of Echinococcus multilocularis.

>Full-malaria

MBGD is a database for comparative analysis of completely sequenced microbial genomes, the number of which is now growing rapidly. The aim of MBGD is to facilitate comparative genomics from various points of view such as ortholog identification, paralog clustering, motif analysis and gene order comparison. MBGD is now maintained at National Institute for Basic Biology.

>MBGD

Bacillus subtilis ORF DB by JAFAN (Japan Functional Analysis Network of B. subitlis)

>BSORF

YEBIS is a motif extraction program developed by T. Yada (Kyoto Univ.) et al. It extracts a set of motifs without any a priori knowledge from a number of functionally-related DNA sequences. Using the hidden Markov model, these motifs are represented in a more general form than other conventional methods, such as the weight matrix method. When applied it to several sets of benchmark data, and it was found that YEBIS had comparable capability to the existing methods but was much faster.

>YEBIS

ATTED-II is a database for gene coexpression networks in Arabidopsis. The networks are constructed using publicly available microarray data.

>ATTED-II

COXPRESdb is a database for gene coexpression networks in human, mouse and rat. The networks are constructed using publicly available microarray data.

>COXPRESdb