Table 1. Major Biological Sequence Databases
Database Web Site Comment
Nucleotide Sequences
GenBank1 http://www.ncbi.nlm.nih.gov/Genbank/GenBankSearch.html Primary sequence repository in North America
EMBL1 http://www.ebi.ac.uk/embl/index.html Primary sequence repository in Europe
DDBJ1 http://www.ddbj.nig.ac.jp Primary sequence repository in Japan
Protein Sequences
GenBank http://www.ncbi.nih.gov/entrez/query.fcgi?db=Protein Translated coding regions of nucleotide sequences in GenBank
  - RefSeq http://www.ncbi.nlm.nih.gov/RefSeq/ Expert annotated. Derived from community-submitted data. Non-redundant
  - nr  2 http://www.ncbi.nlm.nih.gov/BLAST/ Composite of GenBank translations+RefSeq+SwissProt+PIR+PRF+PDB
UniProt http://www.pir.uniprot.org/ Composite of SwissProt+TrEMBL+PIR. Many functional annotations
  - UniRef http://www.pir.uniprot.org/database/nref.shtml Similar sequences are clustered
  - UniParc http://www.pir.uniprot.org/database/archive.html Large composite database. Includes predicted proteins from Ensembl
SwissProt http://kr.expasy.org/sprot/ Expert annotated. Many comments, references & feature tables
TrEMBL http://kr.expasy.org/sprot/ Automatic translations of EMBL (not yet integrated in SwissProt)
PIR http://pir.georgetown.edu/ The first international protein database
OWL http://umber.sbs.man.ac.uk/dbbrowser/OWL/ Composite sequence database. Non-redundant
Gene Records
Entrez Gene http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene A single interface to information about genetic loci
Ensembl http://www.ensembl.org/ Automated annotation of genomes
Specialized Genome Databases
Fugu (Puffer Fish) http://fugu.hgmp.mrc.ac.uk/PFW Fugu rubripes.Compact genome compared to other vertebrates
Exofish http://www.genoscope.cns.fr/externe/tetraodon/ Tetraodon nigroviridis.Compact genome compared to other vertebrates
FlyBase http://flybase.bio.indiana.edu Community ressource on genetics, genomics & biology of Drosophila 
WormBase http://www.wormbase.org Community ressource on genetics, genomics & biology of C. elegans
Rat database http://rgd.mcw.edu/ Integrated access to data on genetics, genomics and biology
Mouse database http://www.informatics.jax.org Integrated access to data on genetics, genomics and biology
Microbial genomes http://www.tigr.org/tigr-scripts/CMR2/CMRHomePage.spl Access to all bacterial genome sequences completed to date

1) As part of the International Nucleotide Sequence Database Collaboration,
these databases exchange primary sequence data on a daily basis.

2) Non-redundant (nr): In favor of ensuring completeness, the nr database contains many nearly identical sequences.
Only absolutely identical sequences has been eliminated.