Databases in the WWW
NetResources in Bioinformatics

Databases

  • Links to Databases for Molecular Biologists
  • Another collection of DataBases - check this out in case the current list does not contain the link you are looking for ...
  • TIGR Database (TDB) - The Institute for Genomic Research
  • The TIGR Databases are a collection of curated databases containing DNA and protein sequence, gene expression, cellular role, protein family, and taxonomic data for microbes, plants and humans.
  • Human Genome Database (DoubleTwist)
  • Subscriber-based Human genome Database
  • Human Unidentified Gene-Encoded Large Proteins
  • HUGE - A Database of Human Unidentified Gene-Encoded Large Proteins
  • Human BAC Ends
  • Sequences from the ends of bacterial artificial chromosome (BAC) clones provide highly specific markers
  • The Phytophthora Genome Initiative
  • Phytophthora comprise a group of plant pathogenic organisms (Oomycetes) that attack an extremely broad range of agronomically important species, affecting many major crops worldwide. Their cumulative global damage is estimated at billions of dollars annually.
  • Saccharomyces Genome Database
  • SGDTM is a scientific database of the molecular biology and genetics of the yeast Saccharomyces cerevisiae, which is commonly known as baker's or budding yeast.
  • Yeast Intron DataBase
  • The Yeast Intron DataBase (YIDB) contains currently available information about all introns encoded in the nuclear and mitochondrial genomes of the yeast Saccharomyces cerevisiae.
  • Database of Arabidopsis thaliana Annotation
  • All annotated Coding sequences from Arabidopsis Genomic DNA Sequencing are in this Database.
  • ZmDB: Maize Genome Database
  • ZmDB (Zea mays DataBase) website, home of the NSF project Maize Gene Discovery, DNA Sequencing, and Phenotypic Analysis.
  • TRIPLES DataBase
  • database of TRansposon-Insertion Phenotypes, Localization, and Expression in Saccharomyces
  • The Intronerator
  • ntronerator - a collection of tools for exploring the molecular biology and genomics of C. elegans with a special emphasis on alternative splicing.
  • FIMM - A database of functional molecular immunology
  • FIMM, is an integrated database of functional immunology, focusing on MHC, antigens, and diseases.
  • INE (Rice Genome)
  • INtegrated rice genome Explorer - a database integrating the genetic map, physical map and sequencing information of rice genome.
  • The UK Crop BioInformatics Network, UK CropNet
  • Established in 1996 as part of the BBSRC's Plant and Animal Genome Analysis special initiative, our focus is the development, management and distribution of information relating to comparative mapping and genome research in crop plants.
  • Arabidopsis Genome Resource (AGR)
  • AGR is a database developed at NASC using the ACEDB database system. Sequences, maps, and other information has been combined to form a large and powerful information resource.
  • MGI 2.3 - Mouse Genome Informatics (MGI) Home Page
  • The overall goal of the Mouse Genome Sequence (MGS) project is to integrate emerging mouse genomic sequence data with the genetic and biological data available in MGD and GXD. MGS is part of the informatics infrastructure needed to support mouse-human comparative genomics.
  • MGI 2.3 - Gene Expression Menu
  • Mouse Gene Expression Information Resource Project.
  • XREF Home Page
  • To cross-reference homologous genes in yeast and human, all yeast ORF protein sequences from the Saccharomyces Genome Database (SGD) were used as queries against a six-frame translation of the human EST subset of the Database of Expressed Sequence Tags (dbEST).
  • WIT Home Page
  • WIT is a www-based system to support the curation of function assignments made to genes and the development of metabolic models.
  • LocusLink Introduction
  • LocusLink provides link to curated sequence and descriptive information about genetic loci. Information on official nomenclature, aliases, sequence accessions, phenotypes, EC numbers, MIM numbers, UniGene clusters, map information, and related web sites.
  • MAGEST top page
  • Maboya ( the ascidian, Halocynthia roretzi ) Gene Expression patterns and Sequence Tags.
  • BODY MAP
  • GeneE xpression Information on various organs or tissues in man and mice.
  • A Xenopus laevis database
  • Axeldb is a database focussing on gene expression in the frog Xenopus laevis
  • RHdb
  • RHdb is a database of raw data used in constructing radiation hybrid maps.
  • MitBASE - Home Page
  • M i t B A S E - a Comprehensive and Integrated Mitochondrial DNA Database.
  • MITOP - Home
  • Database for mitochondria-related genes, proteins and diseases.
  • Sequence Retrieval System - SRS6
  • 5S rRNA DB
  • 5S rRNA Database.
  • tmRNA Website
  • bacterial tmRNA is so-named for its dual tRNA-like and mRNA-like nature. (It's also known as 10Sa RNA or SsrA)
  • tmRDB
  • tmRDB (tmRNA Database) Provides aligned, Annotated and Phylogenetically Ordered Sequences Related to Structure and Function of tmRNA.
  • SRPDB
  • SRPDB (Signal Recognition Particle Database) Provides Aligned, Annotated and Phylogenetically Ordered Sequences Related to Structure and Function of SRP.
  • Ribosomal Database Project II
  • The Ribosomal Database Project (RDP) provides ribosome related data services to the scientific community, including online data analysis, rRNA derived phylogenetic trees, and aligned and annotated rRNA sequences.
  • ssu rRNA database
  • A database on the structure of ssu ribosomal subunit RNA (further abbreviated as ssu rRNA).
  • lsu rRNA database
  • A database on the structure of lsu ribosomal subunit RNA (further abbreviated as lsu rRNA).
  • Subviral RNA Sequences (Lab J-P Perreault)
  • COMPILATION OF SUBVIRAL RNA SEQUENCES.
  • Intron Sequences & Evolution Databases
  • Intron Sequence and Evolution Database.
  • EID - Exon/Intron DB
  • exhaustive database of protein-coding intron-containing genes.
  • ExInt ExonIntron DataBase
  • Exon-Intron database of eukaryotic organisms.
  • WelcomeUTR
  • Sequence collection, deprived from redundancy, of 5' and 3' UTR sequences from eukaryotic mRNA, collection of functional sequence patterns located in 5' or 3' UTR sequences.
  • Non-coding RNA Data Bank
  • Database of non-coding RNAs.
  • PKB - PseudoBase
  • PseudoBase is a collection of RNA pseudoknots.
  • SELEX_DB
  • SELEX_DB is designed for accumulation of experimental data on selected affinity-enriched sequences from different combinatorial libraries.
  • FIMM
  • FIMM, is an integrated database of functional immunology, focusing on MHC, antigens, and diseases.
  • PRINTS (ProteinMotifs)
  • PRINTS is a compendium of protein fingerprints.
  • Blocks WWW Server
  • Blocks are multiply aligned ungapped segments corresponding to the most highly conserved regions of proteins.

  • SMART - Simple Modular Architecture Research Tool
  • SMART, a simple modular architecture research tool: identification of signaling domains. Accurate multiple alignments of 86 domains that occur in signaling proteins have been constructed and used to provide a Web-based tool (SMART: simple modular architecture research tool) that allows rapid identification and annotation of signaling domain sequences. The majority of signaling proteins are multidomain in character with a considerable variety of domain combinations known.
  • The RCSB Protein Data Bank
  • PDB, the single international repository for the processing and distribution of 3-D macromolecular structure data primarily determined experimentally by X-ray crystallography and NMR.
  • Entrez structure query
  • Biomolecule 3D Structure Search.
  • IMB Jena Image Library of Biological Macromolecules
  • IMB Jena Image Library of Biological Macromolecules, access to all structure entries deposited at the Protein Data Bank (PDB) or at the Nucleic Acid Database (NDB).
  • ModBase database of Comparative Protein Structure Models
  • MODBASE, a database of three-dimensional protein models calculated by comparative modeling.
  • ASTRAL Home Page
  • ASTRAL compendium provides databases and tools for analyzing protein structures and sequences, partially derived from, and augments the SCOP: Structural Classification of Proteins database.
  • SCOP: Structural Classification of Proteins
  • The SCOP database, created by manual inspection and abetted by a battery of automated methods, aims to provide a detailed and comprehensive description of the structural and evolutionary relationships between all proteins whose structure is known.
  • Protein Domain Library - SBASE 8
  • domain homologies in a protein or DNA query sequence.
  • Protein Families Database of Alignments and HMMs - Pfam
  • Pfam is a large collection of multiple sequence alignments and hidden Markov models covering many common protein domains.
  • Protein Domain Database - ProDom
  • The ProDom protein domain database consists of an automatic compilation of homologous domains in proteins.
  • Protein Database - SYSTERS Cluster Set
  • searching algorithm SYSTERS (SYSTEmatic Re-Searching) is based on iterative calls of a traditional database search tool like BLASTP or FASTA. The searching algorithm explores the sequence space around a query sequence - called seed - and finds a set of related sequences to this seed - called cluster - which share a strong similarity.
  • ProClass Database
  • The ProClass database is a non-redundant protein database organized according to family relationships as defined collectively by ProSite patterns and PIR superfamilies.
  • Protein Structure Classification - CATH
  • Protein Structure Classification.
  • ProTherm: Thermodynamic Database for Proteins and Mutants
  • Thermodynamic Database for Proteins and Mutants (ProTherm) contains numerical data of several thermodynamic parameters, namely, Gibbs free energy, enthalpy, heat capacity, transition temperature etc. for wild type and mutant proteins, that are important for understanding the structure and stability of proteins upon mutations.
  • Swiss 2d PAGE Database - Nucleic Acids Research 28:286-288
  • SWISS-2DPAGE (http://www.expasy.ch/ch2d/ ) is an annotated two-dimensional polyacrylamide gel electrophoresis (2-DE) database established in 1993.
  • ExPASy - SWISS-2DPAGE
  • Two-dimensional polyacrylamide gel electrophoresis database - SWISS-2DPAGE contains data on proteins identified on various 2-D PAGE reference maps.
  • BioBase at the Danish Centre for Human Genome Research
  • The Danish Centre for Human Genome Research's 2-D PAGE Databases are being developed for functional genome analysis in health and disease. They contain data on proteins identified on various reference maps. You can display protein names and information on specific protein spots by clicking on the image. You can search by protein name, keywords, Mr and pI or organelle or cellular component. Protein files contain extensive links to other databases (MEDLINE, GenBank, Swiss-Prot, PIR, PDB, OMIM, UniGene, GeneCards, etc.) or Web sites.
  • 2D-PAGE DataBase at the MPI Berlin
  • The DataBase contains data from several Mycobacteria strains, Helicobacter pylori, Borrelia garinii and Jurkat T cells. The DB complies with the rules of the world-2D-database and is linked to several sequence databases.
  • Database of Interacting Proteins
  • Database of Interacting Proteins.

  • Codon Usage Database
  • Codon Usage Database is an extended WWW version of CUTG (Codon Usage Tabulated from GenBank). The frequency of codon use in each organism is made searchable through this World Wide Web site.
  • TransTerm - Translational Signal Database
  • TransTerm is a database of sequence contexts about the stop and start codons of many species found in GenBank. TransTerm also contains codon usage data for these same species and summary statistics for the sequences analysed. The 3' and 5' UTR flanking sequences and coding sequences for each organism are also available for searching via our experimental server. We have also have a great deal of other information 'in house' that we have not yet been able to make easily available. Contact the authors if you would like this information before it is available through this interface.
  • Alternative Splicing DB (ASDB) - Main Page
  • The Alternative Splicing DB (ASDB) has been established with the intention of assembling in a central, publicly accessible site information about alternatively spliced genes, their products and expression patterns.
  • Transcription Regulatory Regions Database (TRRD)
  • TRRD is designed for accumulation of experimental data on extended regulatory regions of eukaryotic genes. The TRRD format allows to describe the modular structure of transcription regulatory regions and the hierarchy of theirs constituent regulatory units.
  • Eukaryotic Promoter Database
  • EPD - The Eukaryotic Promoter Database is an annotated non-redundant collection of eukaryotic POL II promoters, for which the transcription start site has been determined experimentally.
  • ExPASy - ENZYME
  • ENZYME is a repository of information relative to the nomenclature of enzymes. It is primarily based on the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (IUBMB) and it describes each type of characterized enzyme for which an EC (Enzyme Commission) number has been provided.
  • Official REBASE Homepage
  • REBASE The Restriction Enzyme Database.

  • Molecular Informatics Resource for the Analysis of Gene Expression
  • MIRAGE (Molecular Informatics Resource for the Analysis of Gene Expression) is a web site dedicated to methodologies, tools, and technologies relating to information in the study of gene expression.
  • Gene Regulatory Sequence Analysis - gresa
  • COMPEL - Database on composite regulatory elements affecting gene transcription in eukaryotes.
  • TRANSFAC - The Transcription Factor Database
  • TRANSFAC - The Transcription Factor Database.
  • NHGRI/NCBI Histone Sequence Database
  • The Histone Database: a comprehensive WWW resource for histones and histone fold-containing proteins.
  • MEROPS - the Peptidase Database
  • MEROPS database provides a wealth of information on proteases. There is a page describing each individual protease as well as one for each of the families into which they can be grouped, and even for each of the clans into which the families can be grouped. Many hundreds of proteases can be found by name, identifier or the organism in which they occur.
  • Aminoacyl-tRNA Synthetase Database - AARS DataBase
  • AminoAcyl-tRNA Synthetases DataBase.

  • NHGRI Homeodomain Resource
  • The Homeodomain Resource is an annotated collection of non-redundant protein sequences, three-dimensional structures, and genomic information for the homeodomain protein family.
  • DExH/PROTEIN DATABASE
  • This database is an attempt to gather information about the DExH/D protein family with particular emphasis on the biochemical and functional characteristics of these proteins. Because DExH/D proteins are essential in numerous fundamental biological processes, research concernig these proteins is conducted in various disciplines such as biochemistry, genetics and biophysics.
  • Sensory Signal Transduction Proteins - SENTRA
  • A Database of Sensory Signal Transduction Proteins.
  • Olfactory Receptor DB - ORDB
  • ORDB is a database of sequences of olfactory receptor proteins.
  • Intein Database (Protein Splicing)
  • Intein Database - Protein splicing is defined as the excision of an intervening protein sequence (the INTEIN) from a protein precursor and the concomitant ligation of the flanking protein fragments (the EXTEINS) to form a mature extein protein and the free intein.
  • Stanford HIV RT and Protease Sequence Database
  • A database linking HIV-1 RT and protease sequence data, drug treatment histories, drug susceptibility, and clinical parameters.
  • Atlas of Genetics and Cytogenetics in Oncology and Haematology
  • Atlas of Genetics and Cytogenetics in Oncology and Haematology.
  • SNP Database
  • Database of Single Nucleotide Polymorphisms.
  • KKIDD - Allele frequency DataBase
  • The ABI Genetic Linkage Panels are being typed in ten worldwide populations by the Kidd Lab, Department of Genetics, Yale University School of Medicine. We will post allele frequencies in this site as soon as they become available. However, it must be noted that these allele frequencies should be used for reference purposes only. Authors wishing to perform statistical analyses on these data should contact Kenneth K. Kidd first.
  • MuationView - (Keio Univ. Dept. Mol. Biol.)
  • Programs (HTML or Java) to visualize mutation distribution. You need to register to gain access.
  • KinMutBase - Disease-causing Mutations in Tyrosine Kinase
  • KinMutBase: A registry of disease-causing mutations in protein kinase domains.
  • KeyNet
  • KEYNET is a database of Keywords extracted from EMBL and GenBank databases. The Keynet structure is based on biological criteria aimed to assist the user in data searching and to minimize the risk of loss of information.
  • Rare BasePair DB (Fox Lab)
  • Database provides rapid access to all the RNA structures in which a particular rare base pair has been found.

  • Biocatalysis/Biodegradation Database
  • Minnesota Biocatalysis/Biodegradation Database Microbial biocatalytic reactions and biodegradation pathways primarily for xenobiotic, chemical compounds.
  • LIGAND Chemical Database for Enzyme Reactions
  • LIGAND - Database for enzymes, compounds, and reactions.

    Sequence Databanks

  • EntrezBrowser
  • Searching GenBank
  • ExPASy Molecular Biology Server
  • The Catalog of Databases
  • NCBI HomePage
  • EMBL Outstation, Hinxton.
  • DNA Data Bank of Japan WWW Title Page
  • KEGG - Kyoto Encyc. of Genes and Genomes
  • Welcome to the National Center for Genome Resources
  • COG
  • MIPS
  • ExPASy - SWISS-PROT and TrEMBL
  • SWISS-PROT + TrEMBL Home Page

  • ProtoMap - Main
  • EcoCyc/MetaCyc Home Page
  • EcoGene Database Home Page
  • REGULONDB
  • EMGLib
  • Micado Main Menu
  • CyanoBase
  • Proteome, Inc: Database registration

  • Beowulf Genomics
  • EcoCyc - E.coli Genes and Metabolism
  • KEGG Functional: Helicobacter pylori
  • KEGG Genome Sequencing Projects
  • TIGR Database (TDB)

  • Proteomics

  • Biovation
  • LSB LargeScaleBiology
  • Oxford GlycoSciences
  • Protana A/S
  • PROT@GEN
  • Proteome, Inc.
  • TopLab
  • Proteome (Hecker, Greifswald)
  • Protein 2D Group
  • SWISS-2DSERVICE
  • 2D GEL DATABASES ON THE INTERNET

  • Genomes

  • Archaeoglobus fulgidus Genome (AFDB)
  • Chlamydia Genome (Berkeley)
  • Chlamydia Plasmid Sequence 1 (Serovar D)
  • Chlamydia Plasmid Sequence 2 (Serovar L2)
  • Helicobacter pylori Genome (J99 ASTRA)
  • Pseudomonas aeruginosa
  • Drosophila melanogaster Genome (Berkeley)
  • Plasmodium falciparum Genome (PfG) - Parasites Database
  • Saccharomyces cerevisiae Genome
  • Trypanosoma brucei Genome - Parasites Database
  • Magpie Sequenzierprojekte
  • American Type Culture Collection

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  • Biotech Rumor Mill
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     ©   Klaus P. Schäfer - Last Update  29.11.2001