MEDALS METI Life science integrated database portal site

ARCHAIC

Summary	The database provides DNA sequences of archaebacterial genomes and their annotation. The aim of ARCHAIC is to analyze archaebacterial genomic DNA sequences (including originally determined ones) in order to understand the overall organization of the genomes and compare different species. Original informatical methods were developed for identifying genes, pseudo-genes, and operons essentially on the basis of a statistical analysis of transcription and translation signals. Three archaes data are available (Pyrococcus sp. OT3, Thermoplasma volcanium GSS1, Archaeoglobus fulgidus).
Data type	DNA-sequence , genome

Summary

The database provides DNA sequences of archaebacterial genomes and their annotation. The aim of ARCHAIC is to analyze archaebacterial genomic DNA sequences (including originally determined ones) in order to understand the overall organization of the genomes and compare different species. Original informatical methods were developed for identifying genes, pseudo-genes, and operons essentially on the basis of a statistical analysis of transcription and translation signals. Three archaes data are available (Pyrococcus sp. OT3, Thermoplasma volcanium GSS1, Archaeoglobus fulgidus).

Data type

DNA-sequence , genome

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ARMLiPDB

Summary	ARMLiPDB is a database of Age Related Expressions of Murine Liver Genes and Proteins.
Data type	Gene expression

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ConfC

Summary	This database extracts this dynamic information from the protein structure being obtained now and is consist of three kinds of sub-database, that is, 1) evolutionary structure change, 2) conformation changes by some binding and 3) structural flexibility, which were individually classified respectively.
Data type	Protein-structure

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Database of genomes and transcriptional regulations for filamentous fungi

Summary	The filamentous fungus, Aspergillus oryzae, plays an important role in the Japanese sake and fermentation industry, and many industrial enzymes are produced by this organism. We hope this database will provide you useful information for your research and industrial applications.
Data type	DNA-sequence

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DB-SPIRE

Summary	This database includes motif sites of all protein structures in PDB, which are assigned from the motif position in the amino acid sequence. In this database, we use the two kinds of the functional motif databases (i.e. PROSITE and BLOCKS), and search the two kinds of the protein sequence in a PDB file, that is, a sequence described in SEQRES line and in ATOM line for the motif positions in the database. Consequently, the database includes four types of motif site data.
Data type	Protein-motif

Summary

This database includes motif sites of all protein structures in PDB, which are assigned from the motif position in the amino acid sequence. In this database, we use the two kinds of the functional motif databases (i.e. PROSITE and BLOCKS), and search the two kinds of the protein sequence in a PDB file, that is, a sequence described in SEQRES line and in ATOM line for the motif positions in the database. Consequently, the database includes four types of motif site data.

Data type

Protein-motif

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DOGAN

Summary	You can get the results of microbial sequence data, gene information (ORF), gene map, motifs, paper as the basis of estimated genes and proteome analysis from DOGAN. This information has been published to confirm the annotater, re-annotation is also in line with the passage of time. In addition, Blast homology search using the service and, DNA cloning service orders.
Data type	DNA-sequence , Proteome

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Evola

Summary	Evola (Evolutionary annotation database) is a database providing ortholog information of H-InvDB human genes. Evola contains orthologs among human and 14 vertebrates (chimpanzee, macaque, mouse, rat, dog, horse, cow, opossum, chicken, zebrafish, medaka, Tetraodon, and fugu). Evolutionary bioligical information such as protein multiple alignments, phylogenetic trees, transcript variants, and the degree of natural selection (dN/dS) are implemented.
Data type	Comparative genomics

Summary

Evola (Evolutionary annotation database) is a database providing ortholog information of H-InvDB human genes. Evola contains orthologs among human and 14 vertebrates (chimpanzee, macaque, mouse, rat, dog, horse, cow, opossum, chicken, zebrafish, medaka, Tetraodon, and fugu). Evolutionary bioligical information such as protein multiple alignments, phylogenetic trees, transcript variants, and the degree of natural selection (dN/dS) are implemented.

Data type

Comparative genomics

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EzCatDB

Summary	The EzCatDB database analyzes and classifies enzyme catalytic mechanisms on the basis of information from literature and data that are derived from entries in the Protein Data Bank (PDB). Each data set contains corresponding enzyme information, such as E.C. number, PDB entries with their annotated ligand information and active site residues, information on catalytic mechanisms, and links to other databases, such as Swiss-prot, CATH, KEGG, PDBsum, and PubMed.
Data type	Protein-structure Enzyme

Summary

The EzCatDB database analyzes and classifies enzyme catalytic mechanisms on the basis of information from literature and data that are derived from entries in the Protein Data Bank (PDB). Each data set contains corresponding enzyme information, such as E.C. number, PDB entries with their annotated ligand information and active site residues, information on catalytic mechanisms, and links to other databases, such as Swiss-prot, CATH, KEGG, PDBsum, and PubMed.

Data type

Protein-structure Enzyme

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GENIUS II

Summary	GENIUS II is an automated database system in which protein coding regions in complete genomes are assigned to known three-dimensional structures.
Data type	Ptotein-sequence amino acid sequence

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GenoBase

Summary	Scope of database (GenoBase) is to understand comprehensively the living-cell system of Escherichia coli K-12 (W3110). Until now, GenoBase is the public repository for Sequence Information, Proteome, Transcriptome, Bioinformatics, and Knowledge based on literature concerning E.coli. The results of the NEDO project was contained.
Data type	Annotation

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