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Databases available


GenBank

The FeatureExtract server has access to the full GenBank flat file release [ftp://ftp.ncbi.nih.gov/genbank]. Our database is kept up to date within two weeks of the main NCBI GenBank database. Notice that virtually all prokaryotic genomes are part of this database.

At the time of writing (March 2005) 14.6 million entries are available in 143 gigabytes of GenBank files.

Selected Eukaryotic genomes

In addition to the main GenBank release FeatureExtract has access to the following eukaryotic genomic builds, which are not part of the main NCBI GenBank database:

  • Fungi
    • Saccharomyces cerevisiae (Baker's Yeast)
    • Schizosaccharomyces pombe (Fission Yeast)
  • Plants
    • Arabidopsis thaliana
  • Vertebrates
    • Canis familiaris (Dog)
    • Gallus gallus (Chicken)
    • Homo sapiens (Human)
    • Mus musculus (Mouse)
    • Rattus norvegicus (Rat)
  • Invertebrates
    • Apis mellifera (Honey bee)
    • Caenorhabditis elegans (Nematode)
    • Drosophila melanogaster (Fruit fly)
  • Other
    • Encephalitozoon cuniculi (An intracellular parasite)

The eukaryotic databases are handled manually. If you would like to see your favorite organism on the list, please send us an email (see below) with a link to the relevant GenBank files.

The Following GenBank entries are in the eukaryotic database:

For details please refer to the NCBI genome FTP site at: ftp://ftp.ncbi.nih.gov/genomes/ and the list of completed eukaryotic genomes (NCBI).
NC_003070       Arabidopsis thaliana chromosome 1, complete sequence.
NC_003071       Arabidopsis thaliana chromosome 2, complete sequence.
NC_003074       Arabidopsis thaliana chromosome 3, complete sequence.
NC_003075       Arabidopsis thaliana chromosome 4, complete sequence.
NC_003076       Arabidopsis thaliana chromosome 5, complete sequence.

NC_003279       Caenorhabditis elegans chromosome I, complete sequence.
NC_003280       Caenorhabditis elegans chromosome II, complete sequence.
NC_003281       Caenorhabditis elegans chromosome III, complete sequence.
NC_003282       Caenorhabditis elegans chromosome IV, complete sequence.
NC_003283       Caenorhabditis elegans chromosome V, complete sequence.
NC_003284       Caenorhabditis elegans chromosome X, complete sequence.

NT_033778       Drosophila melanogaster chromosome 2R, complete sequence.
NT_033779       Drosophila melanogaster chromosome 2L, complete sequence.
NT_033777       Drosophila melanogaster chromosome 3R, complete sequence.
NT_037436       Drosophila melanogaster chromosome 3L, complete sequence.
NC_004353       Drosophila melanogaster chromosome 4 complete sequence.
NC_004354       Drosophila melanogaster chromosome X, complete sequence.

NC_003229       Encephalitozoon cuniculi chromosome II, complete sequence.
NC_003230       chromosome III of strain GB-M1 of Encephalitozoon cuniculi
NC_003231       Encephalitozoon cuniculi chromosome IV, complete sequence.
NC_003232       chromosome V of strain GB-M1 of Encephalitozoon cuniculi
NC_003233       Encephalitozoon cuniculi chromosome VI, complete sequence.
NC_003234       Encephalitozoon cuniculi chromosome VII, complete sequence.
NC_003235       chromosome VIII of strain GB-M1 of Encephalitozoon cuniculi
NC_003236       Encephalitozoon cuniculi chromosome X, complete sequence.
NC_003237       Encephalitozoon cuniculi chromosome XI, complete sequence.
NC_003238       chromosome IX of strain GB-M1 of Encephalitozoon cuniculi
NC_003242       Encephalitozoon cuniculi chromosome I, complete sequence.

NC_001133       Saccharomyces cerevisiae chromosome I, complete sequence.
NC_001134       Saccharomyces cerevisiae chromosome II, complete sequence.
NC_001135       Saccharomyces cerevisiae chromosome III, complete sequence.
NC_001136       Saccharomyces cerevisiae chromosome IV, complete sequence.
NC_001137       Saccharomyces cerevisiae chromosome V, complete sequence.
NC_001138       Saccharomyces cerevisiae chromosome VI, complete sequence.
NC_001139       Saccharomyces cerevisiae chromosome VII, complete sequence.
NC_001140       Saccharomyces cerevisiae chromosome VIII, complete sequence.
NC_001141       Saccharomyces cerevisiae chromosome IX, complete sequence.
NC_001142       Saccharomyces cerevisiae chromosome X, complete sequence.
NC_001143       Saccharomyces cerevisiae chromosome XI, complete sequence.
NC_001144       Saccharomyces cerevisiae chromosome XII, complete sequence.
NC_001145       Saccharomyces cerevisiae chromosome XIII, complete sequence.
NC_001146       Saccharomyces cerevisiae chromosome XIV, complete sequence.
NC_001147       Saccharomyces cerevisiae chromosome XV, complete sequence.
NC_001148       Saccharomyces cerevisiae chromosome XVI, complete sequence.
NC_001224       Saccharomyces cerevisiae mitochondrion, complete genome.

NC_003424	Schizosaccharomyces pombe chromosome I, complete sequence.
NC_003423	Schizosaccharomyces pombe chromosome II, complete sequence.
NC_003421	Schizosaccharomyces pombe chromosome III, complete sequence.
Bee, Human, Chicken, Dog, Mouse and Rat: See the comple list here: contig list [73867 entries, 4.5 mb]


CORRESPONDENCE

Rasmus Wernersson,