Published online 28 November 2016 Nucleic Acids Research, 2017, Vol. 45, Database issue D37–D42
doi: 10.1093/nar/gkw1070
GenBank
Dennis A. Benson, Mark Cavanaugh, Karen Clark, Ilene Karsch-Mizrachi, 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 15, 2016; Revised October 19, 2016; Editorial Decision October 24, 2016; Accepted November 07, 2016
ABSTRACT
GenBank®
(www.ncbi.nlm.nih.gov/genbank/) is a
comprehensive database that contains publicly available
nucleotide sequences for 370 000 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 environmental sampling projects. Most
submissions are made using the web-based BankIt
or the NCBI Submission Portal. GenBank staff assign
accession numbers upon data receipt. Daily data exchange
with the European Nucleotide Archive (ENA)
and the DNA Data Bank of Japan (DDBJ) ensures
worldwide coverage. GenBank is accessible through
the NCBI Nucleotide database, which links to related
information such as taxonomy, genomes, protein
sequences and structures, and biomedical journal
literature in PubMed. BLAST provides sequence
similarity searches of GenBank and other sequence
databases. Complete bimonthly releases and daily
updates of the GenBank database are available by
FTP. Recent updates include changes to policies regarding
sequence identifiers, an improved 16S submission
wizard, targeted loci studies, the ability to
submit methylation and BioNano mapping files, and
a database of anti-microbial resistance genes.
INTRODUCTION
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 submissions of sequence
data from authors and from bulk submissions of
whole-genome shotgun (WGS) and other high-throughput
data from sequencing centers. The U.S. Patent and Trademark
Office also contributes sequences from issued patents.
GenBank participates with the EMBL-EBI 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) (4).
The INSDC partners exchange data daily to ensure that
a uniform and comprehensive collection of sequence information
is available worldwide. NCBI makes GenBank data
available at no cost over the Internet, through FTP and a
wide range of Web-based retrieval and analysis services (5).
RECENT DEVELOPMENTS
Upcoming changes to sequence identifiers
As first described in the release notes for GenBank 199.0 in
December 2013, and discussed in more detail previously (1),
NCBI is phasing out the practice of assigning GI numbers
as sequence identifiers. Since GI numbers were first introduced
in GenBank 81.0 (February 1994), GenBank records
have had both a GI number and an accession.version identifier.
Removing the redundant GI identifiers and retaining
the more human-readable accession.version simplifies the
process of tracking sequences without any loss of functionality.
Therefore, over the coming months we will no longer
assign GI numbers to a gradually growing number of new
sequences. (Current examples of such sequences are unannotated
contigs in WGS and TSA projects.) In addition,
GI numbers will no longer appear in the default flat file
presentations and FASTA definition lines of sequence data
records, whether obtained from the web, API calls, or the
NCBI FTP site. Sequence records with existing GI numbers
will retain them in XML and Abstract Syntax Notation One
(ASN.1) formats, and NCBI services that accept GI numbers
as input will continue to be supported. NCBI will continue
to add support for accession.version identifiers to all
services that currently do not support them. For example,
the E-utilities now accept the parameter idtype, which when
set to ‘acc’, allows these calls to accept accession.version as
input and provide them as output. As this process unfolds,
NCBI will provide additional announcements on our social
*To whom correspondence should be addressed. Tel: +1 301 496 2475, Fax: +1 301 480 9241; Email: sayers@ncbi.nlm.nih.gov
Published by Oxford University Press on behalf of Nucleic Acids Research 2016.
This work is written by (a) US Government employee(s) and is in the public domain in the US.
D38 Nucleic Acids Research, 2017, Vol. 45, Database issue
media platforms and news feeds, as well as in GenBank release
notes.
16S rRNA submission wizard
The 16S rRNA submission wizard, part of the NCBI submission
portal, now offers faster, real-time analysis to assist
submitters of 16S rRNA sequences from prokaryotes
(submit.ncbi.nlm.nih.gov/genbank/help/). Prokaryotic
samples can be from uncultured, environmental sources
or pure cultured strains. Moreover, a wizard for submitting
rRNA sequences and transcribed spacers from all organisms
is being developed. If samples were generated using
next-generation technologies, only assembled sequences
(two or more reads) will be accepted. Sequences submitted
using the wizard will be automatically processed and
checked for chimeras, vector contamination, low quality sequence
and other problems.
Targeted locus studies (TLS)
GenBank is now accepting sequences from targeted loci
studies. These studies often contain large sets of 16S rRNA
sequence or ultra-conserved elements (UCEs). TLS sequences
are given a ‘TLS’ keyword and have accessions similar
to those of Whole Genome Shotgun (WGS) and Transcriptome
Shotgun Assembly (TSA) sequences (see below)
where the four-letter accession prefix begins with ‘K’. For
example, ‘KAAA00000000.1’ represents the master record
for a TLS project that contains contigs with accessions
KAAA01000001–KAAA01169849.
Bacterial average nucleotide identity (ANI)
As part of the NCBI bacterial genome submission process,
GenBank now performs an average nucleotide identity
analysis to investigate whether the asserted organism name
may be incorrect. Using the genomes already in GenBank,
this ANI analysis can report that a genome submitted as
Escherichia coli is actually Salmonella enterica, for example.
However, since the analysis uses the genomes already
in GenBank, it cannot necessarily be performed for all new
genome submissions.
DNA methylation analysis files
GenBank now accepts analysis files derived from SMRT
sequencing provided by Pacific Biosciences (6). These files
summarize the observed patterns of methylation and can
be included as part of the genome assembly submission
or as supplementary file submissions made through
the NCBI Submission Portal. The most common file
type submitted is the motif summary.csv file. A complete
list of the available base modification files received is
provided at ftp.ncbi.nlm.nih.gov/pub/supplementary data/
basemodification.csv. The list provides for each file the Nucleotide
or Sequence Read Archive (SRA) accessions for the
target sequence, along with BioProject and BioSample accessions,
the source organism, and the URI to the data file
itself.
BioNano genome map files
GenBank now accepts whole genome maps produced
by BioNano mapping technology (7,8). These files can
be used in a variety of genomic analyses, including de
novo assembly, structural variant detection, and assembly
curation, and they can be submitted as supplementary
file submissions through the NCBI Submission Portal.
A complete list of the available BioNano map files is
provided at ftp.ncbi.nlm.nih.gov/pub/supplementary data/
bionanomaps.csv. The list provides for each file the supplementary
files accession number (e.g. SUPPF 0000000066),
the genome accession number (if there is a public genome
assembly in GenBank), the BioProject and BioSample accessions,
the source organism, and the URI to the data file
itself.
Anti-microbial resistance data
As part of the NCBI Pathogen Detection project,
NCBI is now accepting submissions of beta-lactamase
sequences as supplementary data for either WGS
genome submissions or submissions of novel betalactamase
sequences (www.ncbi.nlm.nih.gov/pathogens/
submit beta lactamase/). Beta-lactamase antibiograms
should also be submitted, and these will be linked to
the BioSample record associated with the submission
(www.ncbi.nlm.nih.gov/biosample/docs/beta-lactamase/).
ORGANIZATION OF THE DATABASE
GenBank divisions
GenBank assigns sequence records to 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 five high-throughput divisions
(EST, GSS, HTC, HTG, STS). In addition, the PAT
division contains records supplied by patent offices, the
TSA division contains sequences from transcriptome shotgun
assembly projects, and the WGS division contains sequences
from whole genome shotgun projects. The size and
growth of these divisions, and of GenBank as a whole, are
shown in Table 1.
Sequence-based taxonomy
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 ENA and DDBJ and with the valuable assistance
of external advisers and curators (9,10). About 370 000 formally
described species are represented in GenBank, and
the top species (not including those in the WGS and TSA
divisions) are listed in Table 2.
Sequence identifiers
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 collaborating
Nucleic Acids Research, 2017, Vol. 45, Database issue D39
Table 1. Growth of GenBank divisions (nucleotide base-pairs)
Division Description Release 215 (August 2016) Annual Increase (%)*
TSA Transcriptome shotgun data 103 399 724 586 49.1%
WGS Whole genome shotgun data 1 637 224 970 324 40.7%
BCT Bacteria 26 474 028 571 36.9%
PHG Phages 270 541 687 28.7%
PLN Plants 14 705 679 094 22.9%
VRL Viruses 2 973 938 989 19.2%
PRI Primates 7 802 428 126 14.6%
PAT Patent sequences 17 128 458 325 10.2%
UNA Unannotated 204 984 9.3%
ENV Environmental samples 5 218 628 157 7.7%
INV Invertebrates 16 241 123 317 5.4%
SYN Synthetic 1 045 567 653 4.4%
VRT Other vertebrates 6 917 600 814 4.1%
HTG High-throughput genomic 27 630 729 177 2.1%
MAM Other mammals 3 647 546 848 1.5%
HTC High-throughput cDNA 682 400 482 1.3%
ROD Rodents 4 502 193 236 0.4%
EST Expressed sequence tags 42 516 725 239 0.4%
GSS Genome survey sequences 25 696 517 526 0.3%
STS Sequence tagged sites 640 833 351 0.0%
TOTAL All GenBank sequences 1 944 719 840 486 36.8%
*Measured relative to Release 209 (8/2015).
Table 2. Top organisms in GenBank (release 215)
Organism Base pairs*
Homo sapiens 18 313 373 647
Mus musculus 10 031 175 251
Rattus norvegicus 6 528 259 145
Bos taurus 5 414 550 206
Zea mays 5 207 478 336
Sus scrofa 4 896 632 524
Hordeum vulgare 3 235 262 275
Danio rerio 3 183 146 925
Ovis canadensis 2 590 574 434
Triticum aestivum 1 941 609 064
Cyprinus carpio 1 836 265 727
Solanum lycopersicum 1 745 709 667
Oryza sativa Japonica Group 1 641 275 254
Apteryx australis 1 595 400 865
Strongylocentrotus purpuratus 1 436 120 930
Macaca mulatta 1 335 500 855
Spirometra erinaceieuropaei 1 264 190 782
Xenopus tropicalis 1 250 099 171
Arabidopsis thaliana 1 204 613 994
Nicotiana tabacum 1 202 887 576
*Excludes sequences from chloroplasts, mitochondria, metagenomes, uncultured organisms, WGS and TSA.
databases (GenBank, DDBJ, ENA). 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 suffix
of the accession number, and this Accession.version identifier
appears on the VERSION line of the GenBank flat
file. Beginning with an initial version of ‘.1’, each change
to the sequence data causes the version suffix to increment.
The accession portion of the identifier remains unchanged
and will always retrieve the most recent version of
the record; the older versions remain available under the old
accession.version identifiers. The Revision History report,
available from the ‘Display Settings’ menu on the default
record view in the Nucleotide database (www.ncbi.nlm.nih.
gov/nuccore/), summarizes the various updates for a given
record, including non-sequence changes. A similar system
tracks changes in the corresponding protein translations
in the Protein database (www.ncbi.nlm.nih.gov/protein/).
These identifiers appear as qualifiers for CDS features in the
FEATURES portion of a GenBank entry, e.g. /protein id
= ‘AAF14809.1’.
Identical protein reports
In 2013, NCBI introduced the non-redundant WP protein
sequences in response to the anticipated rapid growth in
the submission of highly redundant prokaryotic genome sequences
from clinical samples (11). The individual, identical
protein annotations represented by a WP sequence do not
D40 Nucleic Acids Research, 2017, Vol. 45, Database issue
have separate records at NCBI, and so many WP records
link to a set of Nucleotide CDS sequences. To clarify these
relationships, the Protein database provides a record format
called an ‘Identical Protein Report’ linked from the
top of a protein record page. These reports list all protein
annotations identical to the given record along with
the Nucleotide CDS for each sequence. The report is also
available through the E-utility EFetch with &rettype = ipg
(eutils.ncbi.nlm.nih.gov).
Unverified sequences
As reported previously (12), as part of the standard review
process for new submissions, GenBank staff may label sequences
as unverified if the accuracy of the submitted sequence
data or annotations cannot be confirmed. Until the
submitter is able to resolve these problems, the definition
line of the sequence will begin with ‘UNVERIFIED:’ and
the sequence will not be included in BLAST databases. This
treatment is being extended to genomic submissions where
the source organism is uncertain, there is evidence of contamination,
or there are other problems with the data. In
addition to the UNVERIFIED label in the definition line,
a short description of the problems will be entered in the
COMMENT field of the record.
Citing GenBank records
Besides being the primary identifier of a GenBank sequence
record, GenBank accession.version identifiers are also the
most efficient and reliable way to cite a sequence record
in publications. Because searching with a GenBank accession
number (without the version suffix) will retrieve the
most recent version of a record, the data returned from
such searches will change over time if the record is updated.
Therefore, sequence data retrieved today by an accession
may be different from that discussed or analyzed in a paper
published several years ago. We therefore encourage submitters
and other authors to include the version suffix when
citing a GenBank accession (e.g. AF000001.5), since this ensures
that the citation refers to a specific version in time.
BUILDING THE DATABASE
The data in GenBank and the collaborating databases,
ENA and DDBJ, are submitted either by individual authors
to one of the three databases or by sequencing centers as
batches of WGS, TSA, HTG, EST or GSS sequences. Data
are exchanged daily with DDBJ and ENA 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 submissions
(www.ncbi.nlm.nih.gov/genbank/), with the majority
of authors using BankIt or the NCBI Submission Portal
(submit.ncbi.nlm.nih.gov). 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 per 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 contamination,
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 confidential
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 up-
date@ncbi.nlm.nih.gov.
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 submission,
including the program tbl2asn, described at www.ncbi.
nlm.nih.gov/genbank/tbl2asn2.html. Submitters can keep
abreast of updates to tbl2asn by subscribing to the NCBI
submissions RSS feed (www.ncbi.nlm.nih.gov/feed/rss.cgi?
ChanKey=genbanksubmissiontoo).
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 directly into
a series of tabbed forms that allow the submitter to describe
the sequence further without having to learn formatting
rules or controlled vocabularies. Using BankIt, submitters
can submit sets of sequences as well as single sequences. Additionally,
BankIt allows submitters to upload source and
annotation data 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 Vecscreen.
Submission using tbl2asn and the submission portal. Submitters
of large, heavily annotated genomes may find it convenient
to use the command line tool tbl2asn to convert a
table of annotations generated from an annotation pipeline
into an ASN.1 record suitable for submission to GenBank.
These files for WGS genome and TSA submissions are then
transmitted to GenBank through the Submission Portal.
Alternatively, the Submission Portal provides an interface
that accepts WGS and TSA data in FASTA format using
a set of online forms. Now tbl2asn also accepts data in the
GFF3 format.
Notes on particular divisions
Environmental sample sequences (ENV). The ENV division
of GenBank accommodates sequences obtained us-
Nucleic Acids Research, 2017, Vol. 45, Database issue D41
ing environmental sampling methods in which the sequence
is derived directly from the isolate. Records in
the ENV division contain ‘ENV’ keywords and use an
‘/environmental sample’ qualifier in the source feature. Environmental
sample sequences are generally submitted for
whole metagenomic shotgun sequencing experiments or
surveys of sequences from targeted genes, like 16S rRNA.
NCBI continues to support BLAST searches (see below) of
metagenomic ENV sequences, but sequences within WGS
projects are now part of the WGS BLAST database.
Whole genome shotgun sequences. Whole Genome Shotgun
(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 a Nucleotide accession number consisting of a fourletter
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 include links to displays of the individual contigs
in the WGS browser. Contig records have accessions
consisting of the same four-letter prefix as their master accession,
followed by a two-digit version number and a sixdigit
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’. The complete list of WGS
projects is available at www.ncbi.nlm.nih.gov/Traces/wgs/.
Many WGS project sequences do not contain annotation,
and those that do may not have these annotations
tracked from one assembly version to the next, and
so should be considered preliminary. Submitters of genomic
sequences, including WGS sequences, are urged
to use evidence tags of the form ‘/experimental = text’
and ‘/inference = TYPE:text’, where TYPE is one of
a number of standard inference types and text consists
of structured text. Annotation is no longer required for
complete genomes, but we encourage submitters to request
that the genome be annotated by NCBI’s Prokaryotic
Genome Annotation Pipeline (www.ncbi.nlm.nih.gov/
genome/annotation prok/) before being released.
Transcriptome shotgun assembly (TSA) sequences. The
TSA division contains transcriptome shotgun assembly sequences
that are assembled from raw sequence reads deposited
in the Sequence Read Archive (SRA). While SRA
is not part of GenBank, it is part of the INSDC and provides
access to the data underlying these assemblies (13).
TSA records have ‘TSA’ as their keyword and can be retrieved
with the query ‘tsa[properties]’.
RETRIEVING GENBANK DATA
The Entrez system
The sequence records in GenBank are accessible through
the NCBI Entrez retrieval system (14). 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 of population or phylogenetic studies are
also 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 in 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 Learn page
(www.ncbi.nlm.nih.gov/home/learn.shtml).
Associating sequence records with sequencing projects
The BioProject database (www.ncbi.nlm.nih.gov/
bioproject) allows submitters to register large-scale sequencing
projects under a unique project identifier,
enabling reliable linkage between sequencing projects and
the data they produce. A ‘DBLINK’ line appearing in GenBank
flat files identifies the sequencing projects associated
with a GenBank sequence record. In addition, sequence
records may have a link to the BioSample database (15)
that provides additional information about the biological
materials used in the study. Such studies include genome
wide association studies, high-throughput sequencing,
microarrays, and epigenomic analyses. As an example, the
TSA project GBJS contains DBLINK lines that associate
the GenBank sequence record with BioProject record
PRJNA255770 and BioSample record SAMN02928618
as well as the two SRA records containing the raw data,
SRR1522120 and SRR1522122:
BioProject: PRJNA255770
BioSample: SAMN02928618
Sequence Read Archive: SRR1522120,
SRR1522122
In addition to the DBLINK lines for BioProject and
BioSample, GenBank records that represent genome assemblies
will also have a link to the corresponding record in
the Assembly database (16). Assembly records not only collect
metadata and statistics for these genome assemblies, but
also provide a stable accession for the assembly along with
a link to the FTP directory containing the sequence data for
the assembly in GenBank, FASTA, and GFF3 formats.
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 (17,18). BLAST searches may be
performed on the NCBI Web site (19) or by using a set of
standalone programs distributed by FTP (5) .
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 ENA and DDBJ, is available by anonymous FTP from
D42 Nucleic Acids Research, 2017, Vol. 45, Database issue
NCBI at ftp://ftp.ncbi.nlm.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 ftp://ftp.ncbi.nlm.
nih.gov/genbank/daily-nc/. For convenience in file transfer,
the data are partitioned into multiple files; for release 215
there are 2695 files requiring 790 GB of uncompressed disk
storage. A script is provided in ftp://ftp.ncbi.nlm.nih.gov/
genbank/tools/ to convert a set of daily updates into a cumulative
update.
MAILING ADDRESS
GenBank, National Center for Biotechnology Information,
Building 45, Room 6AN12D-37, 45 Center Drive,
Bethesda, MD 20892, USA.
ELECTRONIC ADDRESSES
www.ncbi.nlm.nih.gov––NCBI Home Page.
gb-sub@ncbi.nlm.nih.gov––Submission of sequence data
to GenBank.
update@ncbi.nlm.nih.gov––Revisions to, or notification of
release of, ‘confidential’ GenBank entries.
info@ncbi.nlm.nih.gov––General information about
NCBI resources.
CITING GENBANK
If you use the GenBank database in your published research,
we ask that this article be cited.
FUNDING
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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