Genetic Databases - "The big three" daily updating each other:

NCBI homepage The national center of biotechnology information, USA.

EMBL server European Molecular Biology Laboratory, gene and genomic databases

DDBJ homepage DNA databank of Japan; japanese database.

Largest databases of DNA, RNA and protein sequences. Also provide access to literature and many tools for analysing genetic or protein information, such as BLAST. NCBI also has a genome map browser, taxonomy browser, 3D molecular structure viewer, and many more.
These databases synchronise their content on a daily basis.

Smaller and more specialised databases:

UCSC Genome Bioinformatics Group of the U of California

Access to a large genome collection. Also has genome browser, gene sorter, proteome browser. Allows a "virtual PCR" using primer sequences, outputting matching sequences.

ENCODE Sub-project of UCSC for the human genome

Has the entire human genome with genome browser and all of the tools available at the UCSC site.

Ensembl The Ensembl project

Database of selected metazoan species, mainly vertebrates. Also provides BLAST/BLAT tools.

Wormbase - Biology and genome of C. elegans

Biology and genome of the nemertean Caenorhabditis elegans. Also provides a genome browser and genetic maps, synteny tools, BLAST/BLAT and more.

Mitochondrial Genome databases:

OGRe (OGRe McMaster database)

Database of mitochondrial genomes. Allows browsing species alphabetically or by taxonomy, also provides tools for gene comparison and alignment.

Mitome (Mitochondrial genome Database)

"Dynamic and interactive database for comparative mitochondrial genomics in metazoan animals". Allows comparative analysis and pattern searching. Korean University, therefore sometimes questionable English.

Metamiga (Metazoan Mitochondrial Genomes Accessible Database)

Concentrates on arthropodan mitochondrial genomics. Also provides a (graphical) taxonomy browser and tools such as BLAST and PHRED.

Taxonomic databases:

ITIS - Integrated taxonomic database

Up-to date taxonomy, taxonomic names and synonyms.

TOL Tree of Life project

Biodiversity project that aims at compiling information and pictures of every species and group of organisms. Browsable tree.

iTOL Interactive Tree of Life

Interactive site that lets you zoom in and out on the phylogenetic tree. Also displays information on genome sizes. Currently 191 species (April 2010).

Other databases

Gene Ontology - Project that aims at standardising the representation of genetic information across species and databases

Extensive meta-database that allows browsing and searches in most of the other databases with many options such as filtering by species, gene product function or data sources. Also provides BLAST and analysis and annotation tools.