Various Databases related to Biotechnology

Database

• DBGET (Genome Net)
• Entrez (NCBI)Cool
• DDBJ (DNA data bank of Japan; National Institute of Genetics)
• ATCC (American Type Culture Collection)
• Bacterial Nomenclature Up-To-Date
• List of Bacterial Names with Standing in Nomenclature
• FGSC (Fungal Genetics Stock Center)
• JCRB (Japan Cancer Research Resources Bank):
  Gene Bank (Search)
  Cell Bank
  
• WFCC World Data Center for Microorganisms (WDCM)
  • JCM (Japan Collection of Microorganisms)
    search by name | accession number | culture collection key
  • JFCC (Japan Federation for Culture Collections)
• Network Browser for Databanks in Molecular Biology (SRS)
• EBI (European Bioinformatics Institute)
• Kyoto Encyclopedia of Genes and Genomes (KEGG)
• Human Proteomics Initiative

Nucleic acid database

• CUTG - searchable index of codon usage tables
• EPD (Eukaryotic Promoter Database): EBI | Genome Net
• dbEST (Expressed Sequence Tags)
• OMIM (Online Mendelian Inheritance in Man)
• REBASE (Restriction Enzyme Database)
• MicroArray (Microarray database)
• Array Express (Microarray database)

• Ribosome: RDP (The Ribosomal Database Project) | The rRNA WWW Server
• TFD (Transcription Factor Database)
• Vector db
• 16SMDB, 23SMDB(E. coli 16S & 23S rRNA)
• Small RNA DB
• SRPDB (protein & RNA sequences, secondary structures, and literatures of signal recognition particle)
• uRNADB (U snRNA)
• The RNase P Database
• The RNA Modification DB
• 5S rRNA
• Sequences & secondary structures of Group I intron, 16S, & 23S rRNA
• The RNA World

Protein database

• 2D gel protein databases (QUEST)
• 2D gel protein databases
• The AAA Superfamily - ATPases associated with various cellular activities
• EC-Enzyme - an enzyme classification database
• GuessProt - a tool which allows the retrieval of the SWISS-PROT entries closest to a given pI and Mw.
• Histo - dedicated to the investigation of the relationship between sequence, structure and function of the proteins of the Major Histocompatibility Complex (MHC)
• NRL_3D - a sequence-structure database
• BRENDA - The Comprehensive Enzyme Information System
• OWL - a non-redundant composite of 4 publicly-available primary sources: SWISS-PROT, PIR (1-3), GenBank (translation) and NRL-3D
• PDB database search (Molecules R US)Cool
• SCOP - Structural Classification of Proteins
• FSSP (Fold classification based on Structure-Structure alignment of Proteins)
• HSSP - Homology-derived StrutureS of Proteins
• Chaperones
• Cytokines and receptors
• Cytochrome450
• EF-hand calcium-binding proteins
• Esterases
• GCRDB(G-protein-coupled receptor database)
• Glucoamylases
• Glucocorticoid receptors
• Glycosyltransferses
• Homeobox
• HIV protease database
• Kinesins
• Mutator transposons
• RecA
• SNF2
• Prolysis (proteases and protease inhibitors)
• Thyroid hormone receptors
• Topoisomerases
• Membrane protein crystal structures

Database for various species

• AaeDB - Aedes aegypti genomic database
• Bacterial Image Database
• Escherichia coli
  • CGSC (E. coli Genetic Stock Center)
  • EcoCyc (Encyclopedia of E. coli Genes and Metabolism)
  • The E. coli Index
  • Escherichia coli Databank
• BSORF:Bacillus subtilis genome
• CyanoBase:Synechocystis sp. genome
• MBGD: Microbial genome database
• DictycDB:Dictyostelium cDNA database
• Human chromosome 21 sequence map
• JST human genome sequencing page
• BodyMap:Expression database of human genes
• GENOTK:Human cDNA database
• p53MDB:p53 mutation database
• FlyBase - a database of genetic and molecular data for Drosophila
• HIDB - The Haemophilus influenzae Rd Genome Database
• HIV Database (Los Alamos Natl. Inst.)
• MycDB - Mycobacterium database
• NRSub - A Non-Redundant Database for Bacillus subtilis
• RATMAP
• SGD - Saccharomyces Genome Database
• YPD - The Yeast Protein Database

Literature database

• AIDS Patent Databases
• JAPAN/MARC Search (1993 vol.13 - 1994 vol.12)
• Japan OPAC (On-line Public Access Catalog) List
• Medline Subset in Molecular Genetics

Compound database

• DrugDB
• Klotho: Biochemical Compounds Declarative Database

Tools for Analysis of Protein/Nucleic Acid Sequence and Structure

Sequence Homology

• FASTA: EBI | Stanford Univ.
• BLAST: Genome Net | NCBI | Stanford Univ.
• Smith & Waterman: EBI
• Multi: GenQuest
• Ensembl: Joint project between the Sanger Center and the EBI for annotation of genome sequences

Protein Structure

• Amino Acid Sequence Motif:
  BLOCKS
  MOTIF (Genome Net)
  PMOTIF
  PROSITE (EBI)
  
• BioMagResBank - a database of NMR-derived protein structures
• pI/Mw - a tool which allows the theoretical pI and Mol.Wt.
• PredictProtein - PHD, TOPITS, MaxHom, EvalSec
• PSORT
• Dali (structure alignment of proteins)
• Sarf2 (structure alignment of proteins)
• TMpred (topology prediction of transmembrane protein)
• papia (PAPIA: Parallel Protein Information Analysis system)

Nucleic Acid Structure

• GRAIL - Exon prediction.
• Oligonucleotide Vital Statistics - answers back length, composition, GC%, Tm, etc.
• Pol3scan - searches the eukaryotic polymerase III intragenic control regions A box and B box
• Primer (PCR Primer Picking)
• ReadSeq - an interface for a sequence format convertor
• Tm Determination - oligonucleotide melting temperature
• Webcutter - an on-line tool for restriction mapping

Virtual Cell

• e-cell:
  virtual cell model

Yamato Lab. Home Page(English) 山登研ホームページ(Japanese)