Difference between revisions of "GenBank"
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*[ftp://ftp.ncbi.nih.gov/genbank/tools/build_gbff_cu.pl 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 [ftp://ftp.ncbi.nih.gov/genbank/tools/doc.build_gbff_cu.html here]. | *[ftp://ftp.ncbi.nih.gov/genbank/tools/build_gbff_cu.pl 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 [ftp://ftp.ncbi.nih.gov/genbank/tools/doc.build_gbff_cu.html here]. | ||
*[ftp://ftp.ncbi.nih.gov/genbank/tools/ffidx.pl ffidx.pl] — Generate an index file containing the sequence identifier and byte-offset of each record in a flatfile which contains biological sequence data. | *[ftp://ftp.ncbi.nih.gov/genbank/tools/ffidx.pl ffidx.pl] — Generate an index file containing the sequence identifier and byte-offset of each record in a flatfile which contains biological sequence data. | ||
| + | *[http://www.ebi.ac.uk/embl/Documentation/Release_notes/current/relnotes.html EMBL Nucleotide Sequence Database: Release Notes] | ||
==References== | ==References== | ||
Revision as of 22:17, 28 January 2009
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 Statistics | ||||||
|---|---|---|---|---|---|---|
| Release | Date | Loci | Bases | Sequences1 | Size (GB)2 | Size (GB)3 |
| 169.0 | 2008-12-15 | 98,868,465 | 99,116,431,942 | 98,868,465 | 381 | 407 |
| 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 |
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:
- 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
- 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
- ↑ 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.
- ↑ NCBI-GenBank Flat File - Distribution Release Notes ('
gbrel.txt').
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.
- Trace Archive
