Dennis A. Benson, Ilene Karsch-Mizrachi, Karen Clark, David J. Lipman,
James Ostell and Eric W. Sayers*
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health,
Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
Received September 30, 2011; Revised November 14, 2011; Accepted November 17, 2011
contains publicly available nucleotide sequences
for more than 250000 formally described species.
These sequences are obtained primarily through
submissions from individual laboratories and batch
submissions from large-scale sequencing projects,
including whole-genome shotgun (WGS) and envir-
onmental sampling projects. Most submissions
are made using the web-based BankIt or standalone
Sequin programs, and accession numbers are
assigned by GenBank staff upon receipt. Daily data
exchange with the European Nucleotide Archive
(ENA) and the DNA Data Bank of Japan (DDBJ)
ensures worldwide coverage. GenBank is access-
ible through the NCBI Entrez retrieval system,
which integrates data from the major DNA and
protein sequence databases along with taxonomy,
genome, mapping, protein structure and domain
information, and the biomedical journal literature
via PubMed. BLAST provides sequence similarity
searches of GenBank and other sequence data-
bases. Complete bimonthly releases and daily
updates of the GenBank database are available by
FTP. To access GenBank and its related retrieval
and analysis services, begin at the NCBI home
isa comprehensivedatabase that
GenBank (1) is a comprehensive public database of
nucleotide sequences and supporting bibliographic and
biological annotation. GenBank is built and distributed
by the National Center for Biotechnology Information
(NCBI), a division of the National Library of Medicine
(NLM), located on the campus of the US National
Institutes of Health (NIH) in Bethesda, MD, USA.
NCBI builds GenBank primarily from the submission
of sequence data from authors and from the bulk submis-
sion of expressed sequence tag (EST), genome survey
sequence (GSS), whole-genome shotgun (WGS) and
other high-throughput data from sequencing centers.
The US Office of Patents and Trademarks also contributes
sequences from issued patents. GenBank participates with
the EMBL Nucleotide Sequence Database (EMBL-Bank),
part of the European Nucleotide Archive (ENA) (2), and
the DNA Data Bank of Japan (DDBJ) (3) as a partner
in the International Nucleotide Sequence Database
Collaboration (INSDC). The INSDC partners exchange
data daily to ensure that a uniform and comprehensive
collection of sequence information is available worldwide.
NCBI makes the GenBank data available at no cost over
the Internet, through FTP and a wide range of web-based
retrieval and analysis services (4).
In the past year, NCBI redesigned the web interface for
the PopSet database (www.ncbi.nlm.nih.gov/popset) of
related sequences and alignments derived from phylogen-
etic, population, mutation and ecosystem studies that have
been submitted to GenBank. The new PopSet record views
contain three sections: an introduction showing the title
and citation for the citation reporting the data set; a list of
sequences contained in the data set; and, when available,
an alignment of the sequences shown in the same
Graphical Sequence Viewer that is a display option on
nucleotide and protein records. In addition, PopSet
record pages now display links to other PopSet records
reported in the same published study, making it much
easier to locate these related records. For PopSet records
with fewer than 100 sequences, links are provided to
generate a BLAST alignment of the sequences or, if an
alignment was submitted as part of the record, a
distance tree view of the alignment.
New tools for exploring features in GenBank records
Within any NCBI nucleotide or protein sequence record,
the hyperlinks in the feature table section now open a new
tool that highlights that feature in the sequence and
displays details of that annotation. A bar will appear at
*To whom correspondence should be addressed. Tel: +301 496 2475; Fax: +301 480 9241; Email: firstname.lastname@example.org
Nucleic Acids Research, 2012, Vol. 40, Database issue Published online 5 December 2011
Published by Oxford University Press 2011.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/
by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
the bottom of the browser window that allows users to
navigate to other features within the record or to view
the sequence corresponding to the feature in FASTA or
GenBank format. For example, the various segments of a
CDS on a genomic sequence can be highlighted together
and then displayed and downloaded as a single FASTA
record. Sequence records also now have a ‘Find in this
Sequence’ link in the right column that opens a search
bar at the bottom of the browser window. Users can
then input subsequences, including standard ambiguity
codes and nucleotides and Prosite patterns for proteins,
and then locate these patterns within the current sequence.
As part of the standard submission process, GenBank
staff review submissions for biological accuracy and
assist authors in providing accurate annotations. If
GenBank staff is unable to verify the accuracy of the
submitted sequences and/or annotations, they may now
add a comment to the record stating that the sequence is
unverified. Until the submitter is able to resolve the issues,
such sequences will have the word ‘UNVERIFIED:’ at
the beginning of their definition lines and will not be
included in BLAST databases.
Within GenBank, WGS master records (see below)
contain no sequence data, but rather show the descriptive
information and range of accession numbers of the contigs
submitted as part of that WGS project. In the future,
NCBI will no longer assign GI numbers to these individ-
ual contigs, and at that point users will be unable to view
them directly in the Nucleotide database. Instead, users
may view these records in a WGS browser that is linked
from the WGS feature of any WGS master record.
The WGS browser provides the complete descriptive
information from the master record of the project, inter-
active views of the FASTA of every contig record and
also provides links to the FTP files for all the contigs
of the entire project.
ORGANIZATION OF THE DATABASE
GenBank groups sequence records into various divisions
based either on the source taxonomy or the sequencing
strategy used to obtain the data. There are 12 taxonomic
divisions (BCT, ENV, INV, MAM, PHG, PLN, PRI,
ROD, SYN, UNA, VRL, VRT) and six high-throughput
divisions (EST, GSS, HTC, HTG, STS, TSA). Finally,
the PAT division contains records supplied by patent
offices and the WGS division contains sequences from
WGS projects. The size and growth of these divisions,
and of GenBank as a whole, are shown in Table 1.
Database sequences are classified and can be queried
using a comprehensive sequence-based taxonomy (www
.ncbi.nlm.nih.gov/taxonomy/) developed by NCBI in
collaboration with EMBL-Bank and DDBJ and with the
valuable assistance of external advisers and curators.
Almost 250000 formally described species are represented
in GenBank, and the top species in the non-WGS
GenBank divisions are listed in Table 2.
Sequence identifiers and accession numbers
Each GenBank record, consisting of both a sequence and
its annotations, is assigned a unique identifier called an
accession number that is shared across the three collabo-
rating databases (GenBank,DDBJ,EMBL Bank).
Table 1. Growth of GenBank divisions (nucleotide base pairs)
Division DescriptionRelease 185
Transcriptome shotgun data
Whole-genome shotgun data
Genome survey sequences
Expressed sequence tags
Sequence tagged sites
All GenBank sequences
aMeasured relative to Release 179 (8/2010).
Table 2. Top Organisms in GenBank (Release 185)
Organism Non-WGS base pairs
Oryza sativa Japonica Group
Xenopus (Silurana) tropicalis
Canis lupus familiaris
Nucleic Acids Research, 2012,Vol.40, Database issueD49
The accession number appears on the ACCESSION line
of a GenBank record and remains constant over the
lifetime of the record, even when there is a change to the
sequence or annotation. Changes to the sequence data
itself are tracked by an integer extension of the accession
number, and this Accession.version identifier appears on
the VERSION line of the GenBank flat file. The initial
version of a sequence has the extension ‘.1’. In addition,
each version of the DNA sequence is also assigned
a unique NCBI identifier called a GI number that
also appears on the VERSION line following the
VERSION AF000001.5 GI : 7274584
When a change is made to a sequence in a GenBank
record, a new GI number is issued to the updated
Accession.version identifier is incremented. The accession
number for the record as a whole remains unchanged
and will always retrieve the most recent version of the
record; the older versions remain available under the old
A similar system tracks changes in the corresponding
protein translations. These identifiers appear as qualifiers
for CDS features in the FEATURES portion of
Protein sequence translations also receive their own
unique GI number, which appears as a second qualifier
on the CDS feature:
and their originalGI
/db_xref=‘GI : 6513858’
BUILDING THE DATABASE
The data in GenBank and the collaborating databases,
EMBL-Bank and DDBJ, are submitted either by individ-
ual authors to one of the three databases or by sequencing
centers as batches of EST, STS, GSS, HTC, WGS or HTG
sequences. Data are exchanged daily with DDBJ and
EMBL-Bank so that the daily updates from NCBI
servers incorporate the most recently available sequence
data from all sources.
Direct electronic submission
Virtually all records enter GenBank as direct electronic
the majority of authors using the BankIt or Sequin
programs. Many journals require authors with sequence
data to submit the data to a public sequence database as a
condition of publication. GenBank staff can usually assign
an accession number to a sequence submission within two
working days of receipt, and do so at a rate of ?3500/day.
The accession number serves as confirmation that the
sequence has been submitted and provides a means for
readers of articles in which the sequence is cited to
retrieve the data. Direct submissions receive a quality
assurance review that includes checks for vector contam-
ination, proper translation of coding regions, correct
taxonomy and correct bibliographic citations. A draft of
the GenBank record is passed back to the author for
review before it enters the database.
Authors may ask that their sequences be kept confiden-
tial until the time of publication. Since GenBank policy
requires that the deposited sequence data be made public
when the sequence or accession number is published,
authors are instructed to inform GenBank staff of
the publication date of the article in which the sequence
is cited in order to ensure a timely release of the data.
Although only the submitter is permitted to modify
sequence data or annotations, all users are encouraged
to report lags in releasing data or possible errors or
omissions to GenBank at email@example.com.
NCBI works closely with sequencing centers to ensure
timely incorporation of bulk data into GenBank for public
release. GenBank offers special batch procedures for
large-scale sequencing groups to facilitate data submis-
sion, including the program tbl2asn, described at www.
Submission using BankIt
About a third of author submissions are received through
an NCBI web-based data submission tool named BankIt.
Using BankIt, authors enter sequence information and
biological annotations, such as coding regions or mRNA
features, directly into a series of tabbed forms that allow
the submitter to describe the sequence further without
having to learn formatting rules or controlled vocabu-
laries. Additionally, BankIt allows submitters to upload
source and annotation using tab-delimited tables. Before
creating a draft record in the GenBank flat file format for
the submitter to review, BankIt validates the submissions
by flagging many common errors and checking for
vector contamination using a variant of BLAST called
Submission using Sequin and tbl2asn
NCBI also offers a standalone multi-platform submission
program called Sequin (www.ncbi.nlm.nih.gov/projects/
Sequin/) that can be used interactively with other NCBI
sequence retrieval and analysis tools. Sequin handles
simple sequences (such as a single cDNA), phylogenetic
studies, population studies, mutation studies, environmen-
tal samples with or without alignments and sequences with
complex annotation. Sequin has a number of wizards that
guide the submitter in preparing their submission with
proper annotation for a number of data types, like viral
genomic sequences and ribosomal RNA from cultured
and uncultured microbes. Sequin has convenient editing
and complex annotation capabilities and contains a
number of built-in validation functions for quality assur-
ance. In addition, Sequin is able to accommodate large
sequences, such as the 5.6 Mb Escherichia coli genome,
and read in a full complement of annotations from
simple tables. The most recent version, Sequin 11.7, was
released in September 2011 and is available for Macintosh,
PC and Unix computers via anonymous FTP at ftp.ncbi.
nih.gov/sequin. Once a submission is completed, submit-
ters can e-mail the Sequin file to firstname.lastname@example.org
D50 Nucleic Acids Research,2012, Vol.40, Database issue
.nih.gov. Submitters of large, heavily annotated genomes
may find it convenient to use tbl2asn to convert a table
of annotations generated from an annotation pipeline
into an ASN.1 (Abstract Syntax Notation One) record
suitable for submission to GenBank.
Submission of barcode sequences
The Consortium for the Barcode of Life (CBOL) is an
international initiative to develop DNA barcoding as a
tool for characterizing species of organisms using a short
DNA sequence. For animal species, a 648-bp fragment of
the gene for cytochrome oxidase subunit I is used as the
barcode. The plant and fungal communities are using
other loci. NCBI, in collaboration with CBOL (www
.barcoding.si.edu/), provides an online tool (BarSTool)
for the bulk submission of barcode sequences to
barcode) that allows users to upload files containing a
batch of sequences with associated source information.
The Nucleotide query ’barcode[keyword]’ retrieves the
over 500000 barcode sequences in GenBank, over
300000 of which were added in the last year.
Notes on particular divisions
Transcriptome shotgun assembly sequences. The TSA
division contains transcriptome shotgun assembly (TSA)
sequences that are assembled from sequences deposited in
the NCBI Trace Archive, the Sequence Read Archive
(SRA) and the EST division of GenBank. While neither
the Trace Archive nor SRA is a part of GenBank, they
are part of the INSDC and provide access to the data
underlying these assemblies (4,5). TSA records (for
example, EZ000001) have ‘TSA’ as their keyword and
can be retrieved with the query ‘tsa[properties]’.
sample sequences (ENV) division of GenBank accommo-
dates sequences obtained via environmental sampling
methods in which the source organism is unknown.
Many ENV sequences arise from metagenome samples
derived from microbiota in various animal tissues, such
as within the gut or skin, or from particular environments,
such as freshwater sediment, hot springs or areas of mine
drainage. Records in the ENV division contain ‘ENV’ in
the keyword field and use an ‘/environmental_sample’
qualifier in the source feature.
sample sequences. The environmental
WGS sequences. WGS sequences appear in GenBank
as groups of sequence-overlap contigs collected under
a master WGS record. Each master record represents
a WGS project and has an accession number in the
Nucleotide database consisting of a four-letter prefix
followed by eight zeroes and a version suffix as found in
standard GenBank records. The number of zeroes
increases to nine for WGS projects with one million or
more contigs. Master records contain no sequence data;
rather, they are linked to their set of individual contigs
that can be viewed using the new WGS browser (see
above). Contig records have accessions consisting of
the same four-letter prefix as their master accession,
followed by a two-digit version number and a six-digit
contig ID. For example, the WGS accession number
‘AAAA02002744’ is assigned to contig number ‘002744’
of the second version of project ‘AAAA’, whose accession
number is ‘AAAA00000000.2’. Currently, there are over
3400 WGS sequencing projects, many of whose data have
been used to build more than 9 million scaffolds and
chromosomes for genome assemblies. For a complete list
of WGS projects with links to the data, see www.ncbi.nlm
Although WGS project sequences may be annotated,
many low-coverage genome projects do not contain anno-
tation. Because these sequence projects are ongoing and
incomplete, these annotations may not be tracked from
one assembly version to the next and should be considered
preliminary. Submitters of genomic sequences, including
WGS sequences, are urged to use evidence tags of
the form ‘/experimental=text’
TYPE:text’, where TYPE is one of a number of
standard inference types and text consists of structured
Expressed sequence tags. Expressed sequence tags (ESTs)
continue to be a major source of data for gene expression
and annotation studies, and at 39 billion base pairs, it
remains the largest non-WGS division in GenBank. EST
data are available for download from ftp.ncbi.nih.gov/
repository/dbEST/ (6) as well as from the GenBank FTP
site. The data in dbEST are clustered using the BLAST
programs to produce the UniGene database (www.ncbi.
nlm.nih.gov/unigene) of more than 5.3 million gene-
High-throughput genomic and high-throughput cDNA
sequences. The high-throughput genomic (HTG) division
of GenBank (www.ncbi.nlm.nih.gov/genbank/htgs/)
contains unfinished large-scale genomic records, which
are in transition to a finished state (7). These records are
designated as belonging to Phases 0–3 depending on the
quality of the data, with Phase 3 being the finished state.
Upon reaching Phase 3, HTG records are moved into
the appropriate organism division of GenBank.
The HTC divisionof
throughput cDNA (HTC) sequences that are of draft
quality but may contain 50-UTRs, 30-UTRs, partial
coding regions and introns. HTC sequences which are
finished and of high quality are moved to the appropriate
organism division of GenBank. A project generating
HTC data is described in Ref. (8).
Special record types
Third party annotation. Third party annotation (TPA)
records are sequence annotations published by someone
other than the original submitter of the primary sequence
record in DDBJ/EMBL/GenBank (www.ncbi.nlm.nih
.gov/genbank/TPA). Each of the current 160000 TPA
records falls into one of three categories: experimental,
in which case there is direct experimental evidence for
the existence of the annotated molecule; inferential,
in which case the experimental evidence is indirect; and
Nucleic Acids Research, 2012,Vol.40, Database issueD51
reassembly, where the focus is on providing a better
assembly of the raw reads. TPA sequences may be
created by assembling a number of primary sequences.
The format of a TPA record (e.g. BK000016) is similar
to that of a conventional GenBank record but includes the
label ‘TPA_exp:’, ‘TPA_inf:’ or ‘TPA_reasm:’ at the
beginning of each Definition Line as well as corresponding
keywords. TPA experimental and inferential records also
contain a Primary block that provides the base ranges
and identifier for the sequences used to build the TPA.
TPA sequences are not released to the public until their
accession numbers or sequence data and annotation
appear in a peer-reviewed biological journal. TPA submis-
sions to GenBank may be made using either BankIt
records. Within GenBank, CON records are used to
represent very long sequences, such as a eukaryotic
chromosome, where the sequence is not complete but
consists of several contig records with uncharacterized
gaps between them. Rather than listing the sequence
the several component sequences. An example of such a
CON record is CM000663 for human chromosome 1.
(CON)recordsfor assembliesof smaller
RETRIEVING GENBANK DATA
The Entrez system
The sequence records in GenBank are accessible through
the NCBI Entrez retrieval system (4). Records from the
EST and GSS divisions of GenBank are stored in the EST
and GSS databases, while all other GenBank records are
stored in the Nucleotide database. GenBank sequences
that are part population or phylogenetic studies are
collected together in the PopSet database, and conceptual
translations of CDS sequences annotated on GenBank
records are available in the Protein database. Each of
these databases is linked to the scientific literature via
PubMed and PubMed Central. Additional information
about conducting Entrez searches is found in the NCBI
Help Manual (www.ncbi.nlm.nih.gov/books/NBK3831/)
and links to related tutorials are provided on the NCBI
Education page (www.ncbi.nlm.nih.gov/Education/).
Associating sequence records with sequencing projects
The ability to identify all GenBank records submitted
by a specific group or those with a particular focus, such
as metagenomic surveys, is essential for the analysis of
large volumes of sequence data. The use of organism
or submitter names as a means to define such a set of
sequences is unreliable. The BioProject database (www
.ncbi.nlm.nih.gov/bioproject), developed at NCBI and
subsequently adopted across the INSDC, allows submit-
ters to register large-scale sequencing projects under a
between sequencing projects and the data they produce.
BioProject, which replaced the Genome Projects database,
is broader in scope than its predecessor and includes
pointers to data from a wide variety of projects deposited
enabling reliable linkage
in any NCBI primary data archive. Sequencing projects
focus on genomes, metagenomes, transcriptomes, com-
parative genomics as well as on particular loci, such as
16S ribosomal RNA. A ‘DBLINK’ line appearing in
GenBank flat files identifies the sequencing projects with
which a GenBank sequence record is associated. As an
example, the DBLINK line below associates a GenBank
sequence record with Project record 18787.
In the future these links will change to reflect the new
18787’. Project record 18787 provides details of the
carolinensis (www.broad.mit.edu/models/anole/). Within
the Entrez system, such a sequence record is linked
directly to the appropriate BioProject record; these links
are bidirectional, so that the BioProject records also link
back to associated sequence records.
BLAST sequence-similarity searching
Sequence-similarity searches are the most fundamental and
frequent type of analysis performed on GenBank data.
NCBI offers the BLAST family of programs (blast.ncbi.
nlm.nih.gov) to detect similarities between a query
sequence and database sequences (9,10). BLAST searches
may be performed on the NCBI website (11) or by using a
set of standalone programs distributed by FTP (4).
Obtaining GenBank by FTP
NCBI distributes GenBank releases in the traditional flat
file format as well as in the ASN.1 format used for internal
maintenance. The full bimonthly GenBank release along
with the daily updates, which incorporate sequence data
from EMBL-Bank and DDBJ, is available by anonymous
FTP from NCBI at ftp.ncbi.nih.gov/genbank. The full
release in flat file format is available as a set of compressed
files with a non-cumulative set of updates at http://ftp.
ncbi.nih.gov/genbank/daily-nc/. For convenience in file
transfer, the data are partitioned into multiple files; for
release 185 there are 1659 files requiring 550 GB of
uncompressed disk storage. A script is provided in ftp.
ncbi.nih.gov/genbank/tools/ to convert a set of daily
updates into a cumulative update.
www.ncbi.nlm.nih.gov: NCBI Home Page.
email@example.com: Submission of sequence data
firstname.lastname@example.org: Revisions to, or notification
of release of, ‘confidential’ GenBank entries.
If you use the GenBank database in your published
research, we ask that this article be cited.
D52 Nucleic Acids Research,2012, Vol.40, Database issue
FUNDING Download full-text
Funding for open access charge: Intramural Research
Program of the National Institutes of Health, National
Library of Medicine.
Conflict of interest statement. None declared.
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