GenBank: The Nucleotide Sequence Database

1. GenBank: The Nucleotide Sequence Database l?J|Ip2W  
Ilene Mizrachi ON q=bI*  
Created: October 9, 2002 9}*<8%PSt,  
Updated: August 22, 2007 aZBb@~
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Summary K! e5
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The GenBank sequence database is an annotated collection of all publicly available nucleotide ZCuLgCP?Z  
sequences and their protein translations. This database is produced at National Center for rUOl+p_47  
Biotechnology Information (NCBI) as part of an international collaboration with the European Molecular +204.Yj?D  
Biology Laboratory (EMBL) Data Library from the European Bioinformatics Institute (EBI) and the DNA X\ bXat+  
Data Bank of Japan (DDBJ). GenBank and its collaborators receive sequences produced in 9W+RUh^W  
laboratories throughout the world from more than 100,000 distinct organisms. GenBank continues to <V_P)b8$1
 
grow at an exponential rate, doubling every 10 months. Release 134, produced in February 2003, 5ON\Ve_H  
contained over 29.3 billion nucleotide bases in more than 23.0 million sequences. GenBank is built E whCX'Vaj  
by direct submissions from individual laboratories, as well as from bulk submissions from large-scale 71(C@/J  
sequencing centers. -lDAxp6p  
Direct submissions are made to GenBank using BankIt [http://www.ncbi.nlm.nih.gov/BankIt/], 1SO!a R#g  
which is a Web-based form, or the stand-alone submission program, Sequin [http:// #yi&-9B  
www.ncbi.nlm.nih.gov/Sequin/index.html]. Upon receipt of a sequence submission, the GenBank staff 1p }:K`#{  
assigns an Accession number to the sequence and performs quality assurance checks. The "CcdwWM  
submissions are then released to the public database, where the entries are retrievable by Entrez or GO<,zOqvU  
downloadable by FTP. Bulk submissions of Expressed Sequence Tag (EST), Sequence Tagged Site n) xLEx,  
(STS), Genome Survey Sequence (GSS), and High-Throughput Genome Sequence (HTGS) data are >jH%n(TcC  
most often submitted by large-scale sequencing centers. The GenBank direct submissions group also 5?M d  
processes complete microbial genome sequences. U,e'vS{  
History RjW< H6a"K  
Initially, GenBank was built and maintained at Los Alamos National Laboratory (LANL). In the early ,UE>@;]  
1990s, this responsibility was awarded to NCBI through congressional mandate. NCBI undertook e|2@z-Sp-  
the task of scanning the literature for sequences and manually typing the sequences into the data- \[yg f6#[  
base. Staff then added annotation to these records, based upon information in the published article. *uG!U%jY)  
Scanning sequences from the literature and placing them into GenBank is now a rare occurrence. %S9YjMR@  
Nearly all of the sequences are now deposited directly by the labs that generate the sequences. waRK$/b (  
This is attributable to, in part, a requirement by most journal publishers that nucleotide sequences k?7V#QW(  
are first deposited into publicly available databases (DDBJ/EMBL/GenBank) so that the Accession op5G}QZ  
number can be cited and the sequence can be retrieved when the article is published. NCBI began ~8l(,N0  
1-1 yuA+YZ  
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NCBI Handbook GenBank pS6p}S=1]  
accepting direct submissions to GenBank in 1993 and received data from LANL until 1996. Cur- M|DVFC  
rently, NCBI receives and processes about 20,000 direct submission sequences per month, in kACgP!~/1  
addition to the approximately 200,000 bulk submissions that are processed automatically. vv0+F6 @  
International Collaboration ckhU@C|=*  
In the mid-1990s, the GenBank database became part of the International Nucleotide Sequence 7uq/C#N  
Database Collaboration with the EMBL database (European Bioinformatics Institute [http:// [QZ g=."  
www.ebi.ac.uk/], Hinxton, United Kingdom) and the Genome Sequence Database (GSDB; LANL, aTLu7C\-e  
Los Alamos, NM). Subsequently, the GSDB was removed from the Collaboration (by the National R q |,@  
Center for Genome Resources, Santa Fe, NM), and DDBJ [http://www.ddbj.nig.ac.jp/] (Mishima, Vz @2_k   
Japan) joined the group. Each database has its own set of submission and retrieval tools, but the R!Lh~~@{(  
three databases exchange data daily so that all three databases should contain the same set of (2uF<$7(  
sequences. Members of the DDBJ, EMBL, and GenBank staff meet annually to discuss technical T0TgV  
issues, and an international advisory board meets with the database staff to provide additional [@;q#.}Z  
guidance. An entry can only be updated by the database that initially prepared it to avoid conflicting ;U)xZ _Ew~  
data at the three sites. xmXuBp:M(R  
The Collaboration created a Feature Table Definition [http://www.ncbi.nlm.nih.gov/collab/FT/ O3KTKL]  
index.html] that outlines legal features and syntax for the DDBJ, EMBL, and GenBank feature tables. #AO?<L  
The purpose of this document is to standardize annotation across the databases. The presentation ATzFs]~K;  
and format of the data are different in the three databases, however, the underlying biological infor- wSd|-e  
mation is the same. l' mdj!{&  
Confidentiality of Data 1"yr`,}?8r  
When scientists submit data to GenBank, they have the opportunity to keep their data confidential r?2EJE2{V  
for a specified period of time. This helps to allay concerns that the availability of their data in Gen- mxEni y  
Bank before publication may compromise their work. When the article containing the citation of the \`U=pZJ  
sequence or its Accession number is published, the sequence record is released. The database J:Idt}@z  
staff request that submitters notify GenBank of the date of publication so that the sequence can be PK).)5sW  
released without delay. The request to release should be sent to gb-admin@ncbi.nlm.nih.gov. NpLZ ,|H  
Direct Submissions ;_p$5GVR|  
The typical GenBank submission consists of a single, contiguous stretch of DNA or RNA sequence [jEZ5]%  
with annotations. The annotations are meant to provide an adequate representation of the biological B? Z_~Bf&  
information in the record. The GenBank Feature Table Definition [http://www.ncbi.nlm.nih.gov/col- Lm3~< vP1e  
lab/FT/index.html] describes the various features and subsequent qualifiers agreed upon by the ? FlQ\q  
International Nucleotide Sequence Database Collaboration. N H'Dz6K5  
Currently, only nucleotide sequences are accepted for direct submission to GenBank. These wQ9?Z.-$  
include mRNA sequences with coding regions, fragments of genomic DNA with a single gene or U!i1~)s  
multiple genes, and ribosomal RNA gene clusters. If part of the nucleotide sequence encodes a G _-JR  
1-2 ^).  
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NCBI Handbook GenBank 5=_bK^Am  
protein, a conceptual translation, called a CDS (coding sequence), is annotated. The span of the 8I[=iU7]l  
CDS feature is mapped to the nucleotide sequence encoding the protein. A protein Accession num- Qo~|[]GE  
ber (/protein_id) is assigned to the translation product, which will subsequently be added to the b4&l=^:e=  
protein databases. 74r$)\q  
Multiple sequences can be submitted together. Such batch submissions of non-related sequen- *7o@HBbF  
ces may be processed together but will be displayed in Entrez (Chapter 15) as single records. |Kb m74 Z%  
Alternatively, by using the Sequin submission tool (Chapter 12), a submitter can specify that several \q@Co42n\  
sequences are biologically related. Such sequences are classified as environmental sample sets, s}F.D^^G  
population sets, phylogenetic sets, mutation sets, or segmented sets. Each sequence within a set N*+L'bO  
is assigned its own Accession number and can be viewed independently in Entrez. However, with Ggry,3X3  
the exception of segmented sets, each set is also indexed within the PopSet division of Entrez, thus Lpohc4d[V  
allowing scientists to view the relationship between the sequences. zY9CoadZ  
What defines a set? Environmental sample, population, phylogenetic, and mutation sets all #&X5Di[A  
contain a group of sequences that spans the same gene or region of the genome. Environmental ot0 g@q[3  
samples are derived from a group of unclassified or unknown organisms. A population set contains *ze,
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sequences from different isolates of the same organism. A phylogenetic set contains sequences &F:%y(;{Y  
from different organisms that are used to determine the phylogenetic relationship between them. @ZRg9M:N  
Sequencing multiple mutations within a single gene gives rise to a mutation set. >n3ig~0d  
All sets, except segmented sets, may contain an alignment of the sequences within them and fV2w &:^3  
might include external sequences already present in the database. In fact, the submitter can begin 0t[ 1#!=k  
with an existing alignment to create a submission to the database using the Sequin submission tool. _Q'f^Kj  
Currently, Sequin accepts FASTA+GAP, PHYLIP, MACAW, NEXUS Interleaved, and NEXUS Con- ~ mzX1[  
tiguous alignments. Submitted alignments will be displayed in the PopSet section of Entrez. 85
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Segmented sets are a collection of noncontiguous sequences that cover a specified genetic *cZ7?  
region. The most common example is a set of genomic sequences containing exons from a single fZoQQ[s  
gene where part or all of the intervening regions have not been sequenced. Each member record _Wq;bKG  
within the set contains the appropriate annotation, exon features in this case. However, the mRNA V-3 ;7  
and CDS will be annotated as joined features across the individual records. Segmented sets them- ;l^'g}dQ^  
selves can be part of an environmental sample, population, phylogenetic, or mutation set.