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
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 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
The Grass Genera of the World
The Families of Flowering Plants
The Universal Virus Database (ICTVdB) and VIDE
- World Virus Database
Viruses Online - VIDEdB
ICTVdB - A Universal Virus Database
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
Miscellaneous, e.g. codon usage, profiles (Weizmann)
Prosite (via NIH)
Protein databank (Brookhaven)
REF52 2D Gel Protein Database
REBASE - Restrict. Enzyme Data Base (NEB)
REBASE restriction enzymes
EMBNet (Heidelberg), and
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
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
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
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.
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
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
ExPASY Database entry points
- Annotated protein sequence database
- Dictionary of protein sites and patterns
- SWISS-2DPAGE - Two-dimensional polyacrylamide gel electrophoresis database
- 3D images of proteins and other biological macromolecules
- Enzyme nomenclature database
- SeqAnalRef - Sequence analysis bibliographic reference database
Centers: This is a list of BioInformatics centres working on the Human
(or other species) Genome. (This is the
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
The Johns Hopkins University BioInformatics Web Server
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
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)
Department of Energy (DOE).
Other HIV and AIDS Related Sites
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
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
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
Microscope 3D Database
CNE at University Autonoma of
Madrid provides the scientific community with a searchable volume data base from
Search and Analysis:
This will lead to many search sites.
(A mirror of
Mouse Genome Database
(MGD) is maintained by the
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.
- Access to GenBank:
- Searching GenBank: Text and Similarity searching
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.
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
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
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.
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.
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.
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
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).
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
September 14, 2006 03:16 PM