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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)."
Data type"DNA-sequence , genome"
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ARMLiPDB

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SummaryARMLiPDB is a database of Age Related Expressions of Murine Liver Genes and Proteins.
Data typeGene expression
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ConfC

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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."
Data typeProtein-structure
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DB-SPIRE

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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."
Data typeProtein-motif
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DOGAN

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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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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."
Data typeDNA-sequence
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Evola

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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 typeComparative genomics
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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, information on catalytic mechanisms, and links to other databases, such as Swiss-prot, CATH, KEGG, PDBsum, and PubMed. "
Data typeProtein-structure Enzyme
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GENIUS II

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SummaryGENIUS II is an automated database system in which protein coding regions in complete genomes are assigned to known three-dimensional structures.
Data typePtotein-sequence amino acid sequence
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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."
Data typeAnnotation
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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."
Data type"RNA human full-length cDNA, mRNA"
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HGPD

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Summary"HGPD is a unique database that stores the information of a set of human Gateway entry clones and protein expression data and helps the user to search the Gateway entry clones. In the full-length human cDNA sequencing project (FLJ project at NEDO), nucleotide sequences of approximately 30000 human cDNA clones have been analyzed.(cited from paper http://nar.oxfordjournals.org/cgi/content/abstract/gkn872?ijkey=zKpNqhZH6jrUuzi&keytype=ref)"
Data typeDNA-sequence
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INOH Pathway Database

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Summary"INOH (Integrating Network Objects with Hierarchies) is a pathway database of model organisms including human, mouse, rat and others. In INOH, the term pathway refers to higher order functional knowledge such as relationships among multiple bio-molecules that constitute signal transduction pathways or biological events in general. As most part of this knowledge resides in scientific articles, the database focuses on curating and encoding textual knowledge into a machine-processable form.(the former URL:http://www.inoh.org/)"
Data typeProtein-Proteome
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LEGENDA

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Summary"Legenda is the system to find articles in which any pair of gene names, diseases, and substrates are co-occurred in the abstract in MEDLINE. Co-occurrence of the same types (e.g. genes) can be searched. Legenda has its own gene name dictionary. "
Data type"Journal , Gene, Disease, Substrate"
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Microorganism database system

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SummaryThis database allows users to search microorganisms and to see the various biological information. This database is available only in Japanese.
Data type"Journal old species name (if any), philogenetic position, type strain, isolation origin, chemical components as chemical taxonomic index, substrate availability, energy gain type, accession number of 16S rDNA to DDBJ/EMBL/GenBank and so on."
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NBRC culture catalogue search

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Summary"Microorganisms (15,400 clones) held by NBRC of NITE can be searched. There are four ways to search, the first is NBRC number, the second is keyword, the third is scientific name or numberof other institutions, and last is homology search. The results can provide the scientific name, history, agency numbers, culture conditions and the paper information. In addition, prokaryotic (16SrDNA) and eukaryotic (28rDNA) for the registration of the sequence to confirm the identity resources search from the search sequence information. (Own translation)"
Data typeDNA-sequence
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PCDq

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Summary"PCDq is a human protein complex database with quality check index (QCI), which describes evidence levels as subunits (protein members) of the protein complex. In total, 1,319 human protein complexes were firstly predicted by finding densely connected regions with cluster properties in the PPI network integrated from six PPI data (BIND, DIP, MINT, HPRD, IntAct, and GNP_Y2H). Then they were curated with the literature so that PCDq consists of both known and predicted complexes/subunits. The evidence level for each subunit were also annotated and summarized to a quality check index (QCI) for each protein complex. PCDq can also show the complicated PPI sub-networks in a simple, editable graphical view ""PPI-Map"". "
Data typeInteraction
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PDB-REPRDB

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Summary"PDB-REPRDB is a reorganized database of protein chains from PDB (Protein Data Bank), and provides 'the list of the representative protein chains' and 'the list of similar protein chain groups'.Chains classified into coiled coil proteins or peptides, according to SCOP, are removed from the database."
Data typeProtein-structure protein chain
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PPI view

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Summary"The PPI view displays H-InvDB human protein-protein interaction (PPI)information. PPI data were collected from five major public PPI databases (BIND, DIP, MINT, HPRD, IntAct) and integrated them as a non-redundant PPI dataset. As the result, we got 32,198 human PPIs comprised of 9,268 proteins. (at H-InvDB version 5.0) The PPI view displays proteins which interact with the usersCHR(39) query proteins (or gene products), and provides links to H-InvDB locus view and cDNA view, which guide you to the gene locations and the detailed gene functional annotations of these interacting proteins, respectively.PPI view: http://www.h-invitational.jp/hinv/ppi/ PPI view sample:http://h-invitational.jp/hinv/ppi/ppi_view.cgi?hip=HIP000084307"
Data typeProtein-Proteome
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ProSeg

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SummaryProSeg is a database of local structures of protein segments. ProSeg contains thousands of clusters of protein segments that were classified according to their three-dimensional structural resemblance.
Data typeProtein-motif
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Rat Brain Sections

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Summary"This database provides whole section images of rat brain recorded in ultra high resolution. You can see each neuron if you zoom in the images. The database was created by AIST, Eizou Bijutsuin, and PFU Limited.(cited from the original site)"
Data typeMorphology image
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SEVENS

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Summary"SEVENS database includes G-protein coupled receptors (GPCR) genes with seven transmembrane helices, that are identified with high accuracy from complete genomes of 32 eukaryotes, by a pipeline integrating such software as a gene finder, a sequence alignment tool, a motif and domain assignment tool, and a TMH predictor. "
Data typePtotein-sequence amino acid sequence
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TMBETA-DISC

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Summary"We have developed statistical and SVM based methods for discriminating beta barrel membrane proteins from amino acid sequence. The amino acid composition, residue pair preference and motifs are the major attributes for the program. 5 programs (TMBETADISC-COMP, TMBETADISC-DIPEPTIDE, TMBETADISC-MOTIF, TMBETADISC-SVM, TMBETADISC-RBF) was included in TMBETADISC (cited from the original site)."
Data typeProtein-AminoAcid
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TMBETA-GENOME

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Summary"TMBETA-GENOME is a collection of amino acid sequences for all the completed genomes and the ""annotated beta-barrel membrane proteins (TMBs) using different discrimination algorithms. For each genome, the calculations have been performed with statistical methods and machine learning techniques and the results are accumulated in the database. Web interfaces to discriminate beta-barrel membrane proteins have been provided from this cite( """"TMBETA-DISC"""" and """"TMBETA-SVM"""")."""
Data typeProtein-structure
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TMFunction

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SummaryTMFunction is a database of functional residues in alpha-helical and beta-barrel membrane proteins (cited from the original site).
Data type"Protein-structure , functional residues"
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TOT-DB

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SummaryTOT-DB (The Theileria orientalis Genome Annotation Database) ia a database of the genome information of parasitic protists Theileria orientalis.Genes annotated by an integration of expression data and gene prediction by several software are displayed on the G-integra genome browser.TOT-DB also offers the BLAST homolgy search service and data downloads of the genome sequences and gene annotation of T. orientalis.
Data typeComparative genomics
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TraP

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Summary"The metabolic pathways were compared, such as glycolysis, the TCA cycle, amino acid biosynthesis, and nucleic acid biosynthesis among 7 archaea. It is possible to highlight the differences between different archaea. (cited from the original site)"
Data typeMetabolite repression
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VarySysDB

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Summary"This is a system to search, display, and download our research results on human polymorphism based on publicly available data and annotations of transcripts presented by H-InvDB. It provides information about single nucleotide polymorphisms (SNPs), deletion-insertion polymorphisms (DIPs), short tandem repeats (STRs), single amino acid repeats (SARs), structural variation (or copy number variations: CNVs), and their relations to the genome, transcripts, and functional domains."
Data type-
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