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Biology Resources Guide >> Databases & Ejournals >> Sequence, Structure, and Organism Databases

Sequence, Structure, and Organism Databases

 

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."

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

  • RCSB 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.

  • 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.

  • 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.

  • OMIA: Online Mendelian Inheritance in Animals
    Searchable catalog of genes, inherited disorders and traits in animal species (other than human and mouse).

  • 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
    "Provides views for a variety of genomes, complete chromosomes, sequence maps with contigs, and integrated genetic and physical maps. The database is organized in six major organism groups: Archaea, Bacteria, Eukaryotae, Viruses, Viroids, and Plasmids and includes complete chromosomes, organelles and plasmids as well as draft genome assemblies."

  • Genetics: Organism Index (WWW Virtual Library)
    Includes links to Animal, Insect, Microbe and Plant organism sites.



     

 

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Last modified December 23, 2008
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