Database catalog
Protein( 10/23 )
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ARCHAIC
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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). |
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| Data type | DNA-sequence , genome |
ARMLiPDB
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Summary | ARMLiPDB is a database of Age Related Expressions of Murine Liver Genes and Proteins. |
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| Data type | Gene expression |
ConfC
[ Official site (the link is in prep.) ]
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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. |
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| Data type | Protein-structure |
DB-SPIRE
[ Official site (the link is in prep.) ]
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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. |
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| Data type | Protein-motif |
Database of genomes and transcriptional regulations for filamentous fungi
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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. |
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| Data type | DNA-sequence |
Evola
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Summary | Evola (Evolutionary annotation database) is a database providing ortholog information of H-InvDB human genes. Evola contains orthologs of human and 13 species' genes (chimpanzee, macaque, mouse, rat, dog, horse, cow, opossum, chicken, zebrafish, medaka, Tetraodon, and fugu). Viewers of sequence alignments and phylogenetic trees, transcript variants (Locus maps), and natural selection (dN/dS view) are implemented. Duplicate gene family viewer is also available. |
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| Data type | Comparative genomics |
EzCatDB
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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, and catalytic mechanisms. |
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| Data type | Protein-structure Enzyme |
GENIUS II
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Summary | GENIUS II is an automated database system in which protein coding regions in complete genomes are assigned to known three-dimensional structures. |
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| Data type | Ptotein-sequence amino acid sequence |
GenoBase
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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. |
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| Data type | Annotation |
H-InvDB
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Summary | H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. By extensive analyses of all human transcripts, we provide curated annotations of human genes and transcripts that include gene structures, alternative splicing isoforms, protein functions, etc. |
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| Data type | RNA human full-length cDNA, mRNA |
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