GenBank
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).
Contents
Statistics
- GenBank Flat File Release 161.0 (2007-08-15)
- 76,146,236 loci, 79,525,559,650 bases, from 76,146,236 reported sequences.[3]
- Uncompressed, the Release 161.0 flatfiles require roughly 299 GB (sequence files only) or 319 GB (including the '
short directory', 'index', and the*.txtfiles).
- GenBank Flat File Release 158.0 (2007-02-15)
- 67,218,344 loci, 71,292,211,453 bases, from 67,218,344 reported sequences.[3]
- Uncompressed, the Release 158.0 flatfiles require roughly 251 GB (sequence files only) or 263 GB (including the '
short directory', 'index', and the*.txtfiles).
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:
- 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
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
- ↑ Benton D (1990). "Recent changes in the GenBank On-line Service". Nucleic Acids Research, 18(6):1517–1520.
- ↑ Benton D et al. (2006). "GenBank". Nucleic Acids Research, 34(Database):D16-D20.
- ↑ 3.0 3.1 NCBI-GenBank Flat File Release 158.0 - Distribution Release Notes ('
gbrel.txt') — 2007-02-15.
External links
- GenBank (overview)
- 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.
