GenBank

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The GenBank (aka Genetic Sequence Data Bank) sequence database is an open access, annotated collection of all publicly available nucleotide sequences and their protein translations.[1][2] This database is produced at National Center for Biotechnology Information (NCBI).

Statistics

GenBank Flat File Release Statistics
Release Date Loci Bases Sequences1 Size (GB)2 Size (GB)3
168.0 2008-10-15 96,400,790 97,381,682,336 96,400,790 371 396
166.0 2008-06-15 88,554,578 92,008,611,867 88,554,578 343 366
164.0 2008-02-15 82,853,685 85,759,586,764 82,853,685 321 342
161.0 2007-08-15 76,146,236 79,525,559,650 76,146,236 299 319
158.0 2007-02-15 67,218,344 71,292,211,453 67,218,344 251 263
Source: [3]

1 reported sequences
2 Uncompressed flatfiles, sequence files only
2 Uncompressed flatfiles, including the 'short directory', 'index', and the *.txt files


Note: You can find the current release number by issuing the following commmand: 

lynx --dump ftp://ftp.ncbi.nih.gov/genbank/GB_Release_Number

Selected Eukaryotic genomes

Note: The following 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)

GenBank entries 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).

See the complete list here: contig list (73,867 entries; 4.5 MB).

Flat file features

The following documents describe in detail the features of various flat files:

Index files

The index keys (accession numbers, keywords, authors, journals, and gene symbols.) of an index are sorted alphabetically. Following each index key, the identifiers of the sequence entries containing that key are listed (LOCUS name, division abbreviation, and primary accession number). The division abbreviations are: 

PRI - primate sequences
ROD - rodent sequences
MAM - other mammalian sequences
VRT - other vertebrate sequences
INV - invertebrate sequences
PLN - plant, fungal, and algal sequences
BCT - bacterial sequences
VRL - viral sequences
PHG - bacteriophage sequences
SYN - synthetic sequences
UNA - unannotated sequences
EST - EST sequences (expressed sequence tags)
PAT - patent sequences
STS - STS sequences (sequence tagged sites)
GSS - GSS sequences (genome survey sequences)
HTG - HTGS sequences (high throughput genomic sequences)
HTC - HTC sequences (high throughput cDNA sequences)
ENV - Environmental sampling sequences
CON - Constructed sequences

See also

  • Genome projects
  • TAB file format (aka "gb2tab")
  • build_gbff_cu.pl — Build a non-redundant cumulative GenBank flatfile from a set of GenBank Incremental Update (GIU) flatfiles provided by the NCBI. Documentation can be found here.
  • ffidx.pl — Generate an index file containing the sequence identifier and byte-offset of each record in a flatfile which contains biological sequence data.

References

  1. ↑ Benton D (1990). "Recent changes in the GenBank On-line Service". Nucleic Acids Research, 18(6):1517–1520.
  2. ↑ Benton D et al. (2006). "GenBank". Nucleic Acids Research, 34(Database):D16-D20.
  3. ↑ NCBI-GenBank Flat File - Distribution Release Notes ('gbrel.txt').

External links

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