Biological Database

Biology Databases

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ATCC Agriculture Genome Information Server Blocks WWW server  BioMagResBank Database Gateway
Biomolecule Database Bio-Web Servers Data search via Gopher  Enzyme Database
Enzyme Nomenclature Database Enzyme & Metabolic Pathway Database ExPASY Molecular Biology Server Genome Centers
Genome Database & Centers Human Genome Databases and Centers Genome Database & Centers from other organisms The Q Server
HIV & AIDS Database Human Genome Project Resources Human 2D PAGE Database for Proteome Analysis Hybridoma Data Bank
Biochemical Compounds Declarative Database Microbiology Information Portal Microscope 3D Database Molecular Search & Analysis
Mouse Genome Database NCBI GenBank NIEHS Scientific Database Server NIH Molecular Biology Databases
PROSITE Protein Disease Database John Hopkins Bioinformatics Server QUEST Protein Database Center
The Restriction Enzyme Database Gel Protein Database Structure Classification of Proteins Selkov Metabolic Pathway Diagrams
SWISS-PROT TIGR Database Tree of Life (Phylogeny)  


Accessing Databases at Church Lab, HGS Genetics. This document is intended to serve as a guide to using certain bioinformatics programs. This site is maintained at George M Church Lab, Harvard University. Here is the content of the site.

American Type Culture Collection (ATCC) is a global bioscience organization that provides biological products, technical services, and educational programs to private industry, government, and academic organizationsaround the world. The mission of the ATCC is to acquire, authenticate, and maintain reference cultures, related biological materials, and associated data, and to distribute these to qualified scientists in government, industry, and education.

Accessions to the ATCC Database

Bacteria and Bacteriophages Cell Lines and Hybridomas Filamentous Fungi

Yeast Strains

Plant Viruses

Protozoa/Algae

Animal Viruses

Recombinant DNA Materials

Agriculture Genome Information Server is sponsored by the U.S. Department of Agriculture, the Agricultural Research Service and the National Agricultural Library (NAL). This server lets you browse and search the National Genetic Resources Program genome databases, AGRICOLA, and related biological information.

NAL Genome Databases

ANU Databases ANU Molecular Biology Database Server concerns chiefly sequence analysis, protein structure, and phylogenetic reconstruction. However many other topics are covered as well.

The Australian Grasses databases (in collaboration with ABRS).

  • Pooideae (Poaceae) in Australia [ftp] [www]
  • The Grass Genera of the World [ftp] [www]
  • The Families of Flowering Plants [ftp] [www]
  • The Universal Virus Database (ICTVdB) and VIDE databases

  • ICTVdB - World Virus Database
  • Plant Viruses Online - VIDEdB
  • ICTVdB - A Universal Virus Database
  • Virus Databases On-Line
  • Index Virum - Virus Names
  • French WWW Genomic Servers

  • French WWW genomic service, including Caenorhabditis elegans Database
  • BLAST Database Searches at NCBI
  • CompoundKB database - 981 metabolic intermediate compounds
  • Codon usage tables (major species) & EMBL mirror
  • DNA Data Bank of Japan
  • EC enzyme database
  • EMBL data (Heidelberg)
  • ESTDB - Expressed Sequence Tag Database (TIGR)
  • FASTA Database search program (Virginia)
  • Genbank searches (Indiana)
  • Genbank/Swiss-Prot/Protein/PIR (via NIH)
  • GENETHON Human Genome Centre
  • Mendelian Inheritance in Man (index)
  • Metabolic intermediate compounds
  • Microbial germplasm
  • Miscellaneous, e.g. codon usage, profiles (Weizmann)
  • PIR (Houston)
  • Prosite (via NIH)
  • Protein databank (Brookhaven)
  • REF52 2D Gel Protein Database
  • REBASE - Restrict. Enzyme Data Base (NEB)
  • REBASE restriction enzymes
  • Swiss-Prot: EMBNet (Heidelberg), and ExPASy (Geneva)
  • SWISS-2DPAGE - Two-dimensional Polyacrylamide Gel Electrophoresis Database (Geneva)
  • Various (ICGEB, Italy)
  • Bioloists's Control Panel

    BLOCKS WWW Server is an aid to detection and verification of protein sequence homology. BLOCKS consists of BLOCKS tools, Block Search, Getblock, and Block Maker. They compare a protein or DNA sequence to the current database of protein blocks, retrieve blocks, and create new blocks, respectively. Blocks are multiply aligned ungapped segments corresponding to the most highly conserved regions of proteins. The blocks for the BLOCKS database are made automatically by looking for the most highly conserved regions in groups of proteins represented in the PROSITE-database.These blocks are then calibrated against theSWISS-PROT database to obtain a measure of the chance distribution of matches. Click here to learn more about BLOCKS.

    BioMagResBank Database Gateway: is a database of NMR-derived protein structures, developed and maintained by the University of Wisconsin at Madison. WWW access is provided by NIH as an information service.

    Biomolecules Databases maintained by Harvard Biological Laboratories provides several tools for biology research including sequence and molecular structure databases.

  • Bio-Web Servers Around the World : This page supported by John Hopkins University allows you to link to other Biology web sites around the world.

    Database Search via Gopher is supported by John Hopkins University. Here is its gopher main menu.

    EC Enzyme Database: This Web version of EC Enzyme has hot links among its own entries and to the following Databases:

    • OMIM - Online Mendelain Inheritance in Man
    • SWISS-PROT - The Swiss Protein Database

  • Enzyme Nomenclature Database 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.

  • Enzyme and Metabolic Pathway Database (EMP) includes data relating to two subjects - enzymology and metabolism. The enzymological section includes data on over 70 enzymes classified by EC numbers. The database now includes data on approximately 3000 distinct enzymes.

  • ExPASY Molecular Biology Server: This is the ExPASy WWW molecular biology server of the Geneva University Hospital and the University of Geneva. This server is dedicated to the analysis of protein and nucleic acid sequences as well as 2-D PAGE.

      ExPASY Database entry points

      • SWISS-PROT - Annotated protein sequence database
      • PROSITE - Dictionary of protein sites and patterns
      • SWISS-2DPAGE - Two-dimensional polyacrylamide gel electrophoresis database
      • SWISS-3DIMAGE - 3D images of proteins and other biological macromolecules
      • ENZYME - Enzyme nomenclature database
      • SeqAnalRef - Sequence analysis bibliographic reference database

  • Genome Centers: This is a list of BioInformatics centres working on the Human (or other species) Genome. (This is the mirror site.)

  • Genome Databases and Centers: This site supported by Department of Energy (DOE) provides information concerning genome databases and genomic research centers.

  • GenQuest - The Q Server supported by The Johns Hopkins University BioInformatics Web Server [No Operations] is an integrated interface to the sequence comparison server at the Oak Ridge National Lab designed for rapid and sensitive comparison of DNA and Protein sequence to existing DNA and Protein sequence databases and the rapid retrieval of the full database entries of any sequence found in the course of a search.

  • GenoBase Databases: incorporates EMBL Release 41, SwissPro Release 30, Prosite Release 12.1 and Enzyme databank Release 17.Through a system of tables and various query capabilities, this server provides access to an NIH copy of GenoBase, which is a Prolog-based, object-oriented molecular biology database. This installation incorporates and links the contents of several large datasets, including EMBL and Swiss-Prot. GenoBase, created by Dr. Ross Overbeek and associates at Argonne National Laboratory, is now being used in the Division of Computer Research and Technology at the National Institutes of Health. While operations are still experimental, the developers are now providing a gateway for World Wide Web users to a substantial subset of the data in the GenoBase installation.
  • HIV and AIDS Database: The Human Retroviruses and Aids Database collects, curates, analyzes, and publishes genetic sequences of the human immunodeficiency virus HIV and related species. This database is maintained by Los Alamos National Laboratory in the Theoretical Biology and Biophysics Group and are funded through an interagency agreement between the National Institutes of Health (NIH) and the Department of Energy (DOE).

  • Human Genome Project Resources provides information conecrning human genome research. The resources are supported by several human genome centers. GDB Human Genome Data Base is part of the Resources. Here is an introduction to GDB.

  • Human 2D PAGE Databases for Proteome Analysis

  • Hybridoma Data Bank HDB holds data on various aspects of hybridomas and their immunoreactive products. Information on a hybridoma's construction and the reactivity and non-reactivity of its secreted product is included. In addition, information on the availability of an individual hybridoma and its Mab product are included. Information in the HDB is derived from literature,catalogs and survey forms.
  • Klotho: Biochemical Compounds Declarative Database is part of Washington University Institute for Biomedical Computing's attempt to model biological processes, beginning with biochemistry.

  • List of Bacterial Names The List of Bacterial Names with Standing in Nomenclature is a searchable datababase. It includes alphabetically and chronologically, the official nomenclature of bacteria and the nomenclatural changes as cited in the Approved Lists of Bacterial Names, or published, or validated in the International Journal of Systematic Bacteriology. It is extensively annotated to clarify the Rules which govern the scientific nomenclature.
    Keywords: Bacteria, Nomenclature.

    For more information, see: Int. J. Syst. Bacteriol, 1997, 47, 590-592.

  • Microbiology Information Portal from the Microbiology Forum  : The Microbiology microbes bacteria information.
  • Microscope 3D Database supported by EMBnet, CNE at University Autonoma of Madrid provides the scientific community with a searchable volume data base from the microscopes.
  • Molecular Search and Analysis: This will lead to many search sites. (A mirror of Pedro's search page).

  • Mouse Genome Database (MGD) is maintained by the Mouse Genome Informatics Project at The Jackson Laboratory.

  • NCBI GenBank is maintained by National Center for Biotechnology Information (NCBI). The NCBI is responsible for building, maintaining, and distributing GenBank, the NIH genetic sequence database that collects all known DNA sequences from scientists worldwide. The NCBI is a division of the National Library of Medicine (NLM) and is located on the campus of the National Institutes of Health (NIH) in Bethesda, Maryland.

  • NIEHS Scientific Database Server maintained by National Institute of Environment and Health Science and NIEHS Biology group.

  • NIH Molecular Biology Databases supported by National Institute of Health (NIH) provide specifically relates to DNA and protein sequence database holdings.

  • PROSITE is a method of determining what is the function of uncharacterized proteins translated from genomic or cDNA sequences. It consists of a database of biologically significant sites, patterns and profiles that help to reliably identify to which known family of protein (if any) a new sequence belongs.

  • Protein-Disease Database (PDD) maintained by the NCI. This server is part of the NIMH-NCI Protein-Disease Database project for correlating diseases with proteins observable in serum, CSF, urine and other common human body fluids based on biomedical literature. The relational database of the PDD is designed to answer questions regarding protein patterns found in common body fluids with respect to disease conditions discussed in the literature. Data is being collected and entered into the PDD relational database by LBG/NIMH and others. It may be searched in a variety of ways including looking for normalized protein concentration fold-changes of proteins (for disease states with respect to normal states) as well as other more complex queries. Click her to Access the PDD.

  • Prot-Web - the John Hopkins University Bioinformatics Server is a Collection of Protein Databases which contain links to one another as well as links to other databases around the world.

  • QUEST Protein Database Center is a facility for the construction and analysis of Protein Databases. The data is generated by two-dimensional (2D) electrophoresis of proteins on polyacrylamide gels. The center is located at the Cold Spring Harbor Laboratory (CSHL) on Long Island, New York. Its goal is the construction of protein databases for scientific investigations.

  • REBASE - The Restriction Enzyme Database supported by The Johns Hopkins University BioInformatics Web Server is collection of information about restriction enzymes and methylases.

  • REF52 Gel Protein Database was constructed from REF52 experiments performed on normal and transformed rat cell lines. In the publications described, many of the proteins are identified by name, by subcellular localization and by post-translation modification. The REF52 2D Gel shown via the WWW system is a pH 3.5 - 10 gel run with an acrylamide concentration of 10%. Ten microliters of 196640 dpm of methionine labeled TCA precipitable material was loaded. This database is maintained by QUEST Protein Database Center. Here is biological background of REF52 Gel Protein Database.

  • SCOP - Structure Classification of Proteins aims to provide a detailed and comprehensive description of the structural and evolutionary relationships between all proteins whose structure is known. As such, it provides a broad survey of all known protein folds, detailed information about the close relatives of any particular protein, and a framework for future research and classification.

  • Selkov Metabolic Pathway Diagrams: A set of almost 1000 pathway diagrams from the Selkov Enzyme and Metabolic Pathway (EMP) Database has been put on a World Wide Web server at Argonne National Laboratory. The enzymes displayed on the diagrams are clickable links back to our display pages for the enzymes contained in GenoBase.

  • SWISS-PROT is a curated protein sequence database which strives to provide a high level of annotations (such as the description of the function of a protein, its domains structure, post-translational modifications, variants, etc), a minimal level of redundancy and high level of integration with other databases.

  • TIGR Database maintained at the Institute for Genomic Research. The TIGR Database (TDB) is being developed as a collection of molecular biology databases comprising DNA and protein sequence, gene expression, function, cellular role, isology class, taxonomic and sample collection data. The first database available through TDB is Sequences, Sources, Taxa (SST). Here is SST Taxon Search.

  • Tree of Life (phylogeny) supported by University of Arizona is a system designed to contain information about the phylogenetic relationships of organisms, to link biological information available on the Internet in the form of a phylogenetic navigator, and to illustrate the diversity and unity of groups of living organisms.


     
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    Copyright © 2003
    Bioinformatics Centre , Dept. of Microbiology and Biotechnology Centre
    M.S. University of Baroda, Baroda, India 390002 Phone:91-0265-2794396 , Fax: 91-265-2792508

    Last updated: February 06, 2004 04:17 PM