GenBank: The Nucleotide Sequence Database

1. GenBank: The Nucleotide Sequence Database
Ilene Mizrachi
Created: October 9, 2002
Updated: August 22, 2007
Summary
The GenBank sequence database is an annotated collection of all publicly available nucleotide
sequences and their protein translations. This database is produced at National Center for
Biotechnology Information (NCBI) as part of an international collaboration with the European Molecular
Biology Laboratory (EMBL) Data Library from the European Bioinformatics Institute (EBI) and the DNA
Data Bank of Japan (DDBJ). GenBank and its collaborators receive sequences produced in
laboratories throughout the world from more than 100,000 distinct organisms. GenBank continues to
grow at an exponential rate, doubling every 10 months. Release 134, produced in February 2003,
contained over 29.3 billion nucleotide bases in more than 23.0 million sequences. GenBank is built
by direct submissions from individual laboratories, as well as from bulk submissions from large-scale
sequencing centers.
Direct submissions are made to GenBank using BankIt [http://www.ncbi.nlm.nih.gov/BankIt/],
which is a Web-based form, or the stand-alone submission program, Sequin [http://
www.ncbi.nlm.nih.gov/Sequin/index.html]. Upon receipt of a sequence submission, the GenBank staff
assigns an Accession number to the sequence and performs quality assurance checks. The
submissions are then released to the public database, where the entries are retrievable by Entrez or
downloadable by FTP. Bulk submissions of Expressed Sequence Tag (EST), Sequence Tagged Site
(STS), Genome Survey Sequence (GSS), and High-Throughput Genome Sequence (HTGS) data are
most often submitted by large-scale sequencing centers. The GenBank direct submissions group also
processes complete microbial genome sequences.
History
Initially, GenBank was built and maintained at Los Alamos National Laboratory (LANL). In the early
1990s, this responsibility was awarded to NCBI through congressional mandate. NCBI undertook
the task of scanning the literature for sequences and manually typing the sequences into the data-
base. Staff then added annotation to these records, based upon information in the published article.
Scanning sequences from the literature and placing them into GenBank is now a rare occurrence.
Nearly all of the sequences are now deposited directly by the labs that generate the sequences.
This is attributable to, in part, a requirement by most journal publishers that nucleotide sequences
are first deposited into publicly available databases (DDBJ/EMBL/GenBank) so that the Accession
number can be cited and the sequence can be retrieved when the article is published. NCBI began
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NCBI Handbook GenBank
accepting direct submissions to GenBank in 1993 and received data from LANL until 1996. Cur-
rently, NCBI receives and processes about 20,000 direct submission sequences per month, in
addition to the approximately 200,000 bulk submissions that are processed automatically.
International Collaboration
In the mid-1990s, the GenBank database became part of the International Nucleotide Sequence
Database Collaboration with the EMBL database (European Bioinformatics Institute [http://
www.ebi.ac.uk/], Hinxton, United Kingdom) and the Genome Sequence Database (GSDB; LANL,
Los Alamos, NM). Subsequently, the GSDB was removed from the Collaboration (by the National
Center for Genome Resources, Santa Fe, NM), and DDBJ [http://www.ddbj.nig.ac.jp/] (Mishima,
Japan) joined the group. Each database has its own set of submission and retrieval tools, but the
three databases exchange data daily so that all three databases should contain the same set of
sequences. Members of the DDBJ, EMBL, and GenBank staff meet annually to discuss technical
issues, and an international advisory board meets with the database staff to provide additional
guidance. An entry can only be updated by the database that initially prepared it to avoid conflicting
data at the three sites.
The Collaboration created a Feature Table Definition [http://www.ncbi.nlm.nih.gov/collab/FT/
index.html] that outlines legal features and syntax for the DDBJ, EMBL, and GenBank feature tables.
The purpose of this document is to standardize annotation across the databases. The presentation
and format of the data are different in the three databases, however, the underlying biological infor-
mation is the same.
Confidentiality of Data
When scientists submit data to GenBank, they have the opportunity to keep their data confidential
for a specified period of time. This helps to allay concerns that the availability of their data in Gen-
Bank before publication may compromise their work. When the article containing the citation of the
sequence or its Accession number is published, the sequence record is released. The database
staff request that submitters notify GenBank of the date of publication so that the sequence can be
released without delay. The request to release should be sent to gb-admin@ncbi.nlm.nih.gov.
Direct Submissions
The typical GenBank submission consists of a single, contiguous stretch of DNA or RNA sequence
with annotations. The annotations are meant to provide an adequate representation of the biological
information in the record. The GenBank Feature Table Definition [http://www.ncbi.nlm.nih.gov/col-
lab/FT/index.html] describes the various features and subsequent qualifiers agreed upon by the
International Nucleotide Sequence Database Collaboration.
Currently, only nucleotide sequences are accepted for direct submission to GenBank. These
include mRNA sequences with coding regions, fragments of genomic DNA with a single gene or
multiple genes, and ribosomal RNA gene clusters. If part of the nucleotide sequence encodes a
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NCBI Handbook GenBank
protein, a conceptual translation, called a CDS (coding sequence), is annotated. The span of the
CDS feature is mapped to the nucleotide sequence encoding the protein. A protein Accession num-
ber (/protein_id) is assigned to the translation product, which will subsequently be added to the
protein databases.
Multiple sequences can be submitted together. Such batch submissions of non-related sequen-
ces may be processed together but will be displayed in Entrez (Chapter 15) as single records.
Alternatively, by using the Sequin submission tool (Chapter 12), a submitter can specify that several
sequences are biologically related. Such sequences are classified as environmental sample sets,
population sets, phylogenetic sets, mutation sets, or segmented sets. Each sequence within a set
is assigned its own Accession number and can be viewed independently in Entrez. However, with
the exception of segmented sets, each set is also indexed within the PopSet division of Entrez, thus
allowing scientists to view the relationship between the sequences.
What defines a set? Environmental sample, population, phylogenetic, and mutation sets all
contain a group of sequences that spans the same gene or region of the genome. Environmental
samples are derived from a group of unclassified or unknown organisms. A population set contains
sequences from different isolates of the same organism. A phylogenetic set contains sequences
from different organisms that are used to determine the phylogenetic relationship between them.
Sequencing multiple mutations within a single gene gives rise to a mutation set.
All sets, except segmented sets, may contain an alignment of the sequences within them and
might include external sequences already present in the database. In fact, the submitter can begin
with an existing alignment to create a submission to the database using the Sequin submission tool.
Currently, Sequin accepts FASTA+GAP, PHYLIP, MACAW, NEXUS Interleaved, and NEXUS Con-
tiguous alignments. Submitted alignments will be displayed in the PopSet section of Entrez.
Segmented sets are a collection of noncontiguous sequences that cover a specified genetic
region. The most common example is a set of genomic sequences containing exons from a single
gene where part or all of the intervening regions have not been sequenced. Each member record
within the set contains the appropriate annotation, exon features in this case. However, the mRNA
and CDS will be annotated as joined features across the individual records. Segmented sets them-
selves can be part of an environmental sample, population, phylogenetic, or mutation set.

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