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Biology Resources Guide >>
Databases & Ejournals >> Sequence,
Structure, and Organism Databases
Sequence, Structure, and Organism Databases
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Major Directories of Database Links
Reference Databases
Sequence Databases
Structure Databases
Organism Databases
Major Directories of Database Links
Reference Databases
- Gene Ontology (GO)
"Structured, controlled vocabularies (ontologies) that describe gene products in
terms of their associated biological processes, cellular components and
molecular functions in a species-independent manner."
- BioDirectory.com
"BioDirectory is an extensive hand-curated directory and search engine for Life
and Medical Sciences. " It's "a search engine facility for life scientists whose document corpus is centred on
tens of thousands of web-based HTML and PDF documents which form resources
including among others software tools, databases, tutorials, protocols,
troubleshooting guides, laboratory homepages, corporate pages.
" "The BioDirectory's directory listings are provided by Open Directory and
Bioinformatics.Net and enhanced by Oxford Informatics Ltd."
Sequence Databases
- BLAST
BLAST (Basic Local Alignment Search Tool) compares your sequences with
other ungapped sequences and then ranks the matches statistically. BLAST
is available through both email and the WWW. Check out the online
documentation before submitting a query. A tutorial
for the first time user will teach you to input a sequence into the
Basic BLAST web page, choose a program and database, and examine the
results.
- Entrez
A convenient way to retrieve nucleotide or amino acid sequences from
many databases, as well as obtain related Medline/PubMed abstracts.
- Entrez
Nucleotides
Used to search for related DNA sequence files. Part of the Entrez search
and retrieval system, it's a collection of nucleotide entries from GenBank,
RefSeq, and PDB.
- Entrez
Protein
Used to search for related amino acid sequence files. Contains sequence
data from the translated coding regions from DNA sequences in GenBank,
EMBL and DDBJ as well as protein sequences submitted to Protein Information
Resource (PIR), SWISSPROT, Protein Research Foundation (PRF), and Protein
Data Bank (PDB) (sequences from solved structures).
- GenBank
Contains all known DNA, RNA, and amino acid sequences and supporting
citations and annotations. Provides information related to the sequences,
such as investigator, organism, associated bibliographic citations,
and so on. You can search GenBank on investigator's name, organism,
gene name, or by the GenBank accession number. See Searching
GenBank for various methods of doing text and similarity searches.
- EMBL-EBI Databases
European Bioinformatics Institute (EBI). EBI "manages databases
of biological data including nucleic acid, protein sequences and macromolecular
structures." The EMBL database is similar to GenBank and the DDBJ; information
between the three is exchanged daily. While unnecessary to search EMBL
if you have searched GenBank, EMBL does provide more cross references
to related information (such as motifs, structure, and so on).
- Pfam
Large collection of protein families and domains.
For each protein family "you can look at multiple alignments, view protein domain architectures, examine species distribution, follow links to other databases, and view known protein structures.
- PIR
- International Protein Sequence Database
Contains protein sequences that you might not be able to find easily
in Entrez. The database, organized by homology and taxonomy, also contains
information on function, classification of the protein and organism,
literature references, and sites of biological interest. Hotlinks are
provided to GenBank/EMBL, EC-Enzyme database, and RefBase (citations).
- Swiss-Prot
Protein sequence database. Includes extensive annotations (description
of the function of a protein, its domains structure, post-translational
modifications, variants, etc.), minimal redundancy, and links to other
databases.
Structure Databases
- Brookhaven Protein Data Bank (PDB)
Three-dimensional structure and atomic coordinates of several thousand
molecules. Images can be viewed on screen, or exported and viewed with
a molecular graphics program such as Cn3D
or RasMol.
- Entrez
Structure
"The Structure database or Molecular Modeling Database (MMDB) contains
experimental data from crystallographic and NMR structure determinations.
The data for MMDB are obtained from the Protein Data Bank (PDB). The
NCBI has cross-linked structural data to bibliographic information,
to the sequence databases, and to the NCBI taxonomy." The NCBI
3-dimensional viewer, Cn3D,
can be used to visualize these molecular structures.
- NRL_3D
Sequence/Structure Database
"Makes the sequence information in Protein DataBank (PDB) available
for similarity searches and retrieval and provides cross-reference information
for use with the other PIR Protein Sequence Databases. In constructing
NRL_3D, sequence information is extracted only for residues with resolved
three-dimensional coordinates (as represented in PDB "ATOM" records)
and not for residues that are structurally undefined."
- Swiss 3-D Image
Three dimensional images of hundreds of proteins.
Organism Databases
- Caenorhabditis elegans WWW Server
Has WormBase, founded in 2000, which will initially continue the existing
ACeDB database with a new user interface. It's a repository of mapping,
sequencing and phenotypic information about the C. elegans nematode.
- E. coli Genome Project
UW-Madison project description, how to search, and project publications.
- Flybase: A Database of the
Drosophila Genome
A comprehensive database for information on the genetics and molecular
biology of the fruit fly. Includes data from the Drosophila Genome project
and the literature. Includes data files, documents, indixes, forms,
reports and images.
- TAIR: The Arabidopsis Information
Resource
Comprehensive resource for Arabidopsis thaliana scientific community.
Consists of a searchable relational database. The data can be viewed
using their interactive MapViewer, and analyzed with their tools.
- NCBI: Genomic Biology
Fruit fly, human, malaria parasite, microbial genomes, mouse, rat, plant
genomes, retroviruses, and zebrafish resources.
- OMIM: Online Mendelian Inheritance in Man
Searchable catalog of human genes and genetic disorders with information and references plus extensive links to PubMed and Entrez sequence records.
- Entrez
Genome
" The whole genomes of over 600 organisms can be found in Entrez
Genomes. The genomes represent both completely sequenced organisms and
those for which sequencing is in progress. All three main domains of
life - bacteria, archaea, and eukaryota - are represented, as well as
many viruses and organelles."
- Genetics: Organism
Index (WWW Virtual Library)
Includes links to Animal, Insect, Microbe and Plant organism sites.
- Plant Genome Data and Information
Center
Provides access to a variety of information services and publications
covering many aspects of plant genome mapping. (From National Agricultural
Library).
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