Difference between revisions of "GenBank"

Revision as of 00:42, 25 April 2016

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

Note: You can find the current release number by issuing either of the following commands:

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

Selected genomes

see: IDS for a list of files containing the IDs of completed genomes.

Prokayotes

see: summary.txt for a daily updated list of completed bacterial genomes.
see: plasmids.ids for a list of completed plasmid genomes.

Eukaryotes

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:

• EMBL Features and Qualifiers
• User Manual — by UniProt Knowledgebase (release 10.4; 2007-05-01)
• Protein naming guidelines — by UniProt - Swiss-Prot Protein Knowledgebase (release 52.4; 2007-05-01)

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
WGS - Whole Genome Shotgun sequencing projects

See also

• Genome projects
• GFF file format — format for describing genes and other features associated with DNA, RNA and Protein sequences.
• 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.
• EMBL Nucleotide Sequence Database: Release Notes

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

• GenBank (overview)
• NCBI Resource Guide
• FTP directory containing full GenBank flat file releases (NCBI)
• Genomes (NCBI)
• List of completed eukaryotic genomes (NCBI)
• The DDBJ/EMBL/GenBank Feature Table: Definition — version 6.6, 2006-10.
• Trace Archive