GenBank: The Nucleotide Sequence Database

1. GenBank: The Nucleotide Sequence Database I3[RaZ2z{  
Ilene Mizrachi ?yM/j7Xn  
Created: October 9, 2002 o >4>7  
Updated: August 22, 2007 9kg>)ty@  
Summary fD}]Mi:V  
The GenBank sequence database is an annotated collection of all publicly available nucleotide o>rlrqr?_  
sequences and their protein translations. This database is produced at National Center for 8;BwzRtgT  
Biotechnology Information (NCBI) as part of an international collaboration with the European Molecular T`<k4
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Biology Laboratory (EMBL) Data Library from the European Bioinformatics Institute (EBI) and the DNA ZTz(NS EK  
Data Bank of Japan (DDBJ). GenBank and its collaborators receive sequences produced in f2e$BA  
laboratories throughout the world from more than 100,000 distinct organisms. GenBank continues to w3|.4hS  
grow at an exponential rate, doubling every 10 months. Release 134, produced in February 2003, jN{xpd  
contained over 29.3 billion nucleotide bases in more than 23.0 million sequences. GenBank is built GT}#iM  
by direct submissions from individual laboratories, as well as from bulk submissions from large-scale ,r,;2,;6nd  
sequencing centers. ~(P\F&A(&  
Direct submissions are made to GenBank using BankIt [http://www.ncbi.nlm.nih.gov/BankIt/], Y$5v3E\uc  
which is a Web-based form, or the stand-alone submission program, Sequin [http:// NW Qu-]P  
www.ncbi.nlm.nih.gov/Sequin/index.html]. Upon receipt of a sequence submission, the GenBank staff U1tPw`0h  
assigns an Accession number to the sequence and performs quality assurance checks. The 0~5}F^8[L  
submissions are then released to the public database, where the entries are retrievable by Entrez or R,Uy3N  
downloadable by FTP. Bulk submissions of Expressed Sequence Tag (EST), Sequence Tagged Site .ihn@eg  
(STS), Genome Survey Sequence (GSS), and High-Throughput Genome Sequence (HTGS) data are 4tu>~ vOE  
most often submitted by large-scale sequencing centers. The GenBank direct submissions group also cDol o1*  
processes complete microbial genome sequences. u<r('IW0  
History A+*(Pds  
Initially, GenBank was built and maintained at Los Alamos National Laboratory (LANL). In the early j-E>*N}-_  
1990s, this responsibility was awarded to NCBI through congressional mandate. NCBI undertook Nxk'!:  
the task of scanning the literature for sequences and manually typing the sequences into the data- j-\u_#kx%  
base. Staff then added annotation to these records, based upon information in the published article. oQB1fs  
Scanning sequences from the literature and placing them into GenBank is now a rare occurrence. QZP;k!"w  
Nearly all of the sequences are now deposited directly by the labs that generate the sequences. 3ZZI1_j  
This is attributable to, in part, a requirement by most journal publishers that nucleotide sequences P?ol]MwaB  
are first deposited into publicly available databases (DDBJ/EMBL/GenBank) so that the Accession y`Y}P1y*  
number can be cited and the sequence can be retrieved when the article is published. NCBI began )Em,3I/.l  
1-1 #?|z&
9  
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NCBI Handbook GenBank O/@ [VPf  
accepting direct submissions to GenBank in 1993 and received data from LANL until 1996. Cur- ?E+XD'~  
rently, NCBI receives and processes about 20,000 direct submission sequences per month, in 5mBk[{  
addition to the approximately 200,000 bulk submissions that are processed automatically. j* ja )  
International Collaboration hZG{"O!2s  
In the mid-1990s, the GenBank database became part of the International Nucleotide Sequence 8\_,Y ji  
Database Collaboration with the EMBL database (European Bioinformatics Institute [http:// Ds/zl Z  
www.ebi.ac.uk/], Hinxton, United Kingdom) and the Genome Sequence Database (GSDB; LANL, Z)4P>{  
Los Alamos, NM). Subsequently, the GSDB was removed from the Collaboration (by the National w-/Tb~#E  
Center for Genome Resources, Santa Fe, NM), and DDBJ [http://www.ddbj.nig.ac.jp/] (Mishima, SjU6+|l  
Japan) joined the group. Each database has its own set of submission and retrieval tools, but the L1+cv;t  
three databases exchange data daily so that all three databases should contain the same set of L2tmo-]nw  
sequences. Members of the DDBJ, EMBL, and GenBank staff meet annually to discuss technical =]Bm>67"  
issues, and an international advisory board meets with the database staff to provide additional u^9,u/gj  
guidance. An entry can only be updated by the database that initially prepared it to avoid conflicting Jl}7]cVq#  
data at the three sites. ;T(^riAEl  
The Collaboration created a Feature Table Definition [http://www.ncbi.nlm.nih.gov/collab/FT/ M?97F!\U  
index.html] that outlines legal features and syntax for the DDBJ, EMBL, and GenBank feature tables. s=+
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The purpose of this document is to standardize annotation across the databases. The presentation 0U~JSmj:2K  
and format of the data are different in the three databases, however, the underlying biological infor- Nrh`DyF0D!  
mation is the same. (~4AG \  
Confidentiality of Data n9ih^H  
When scientists submit data to GenBank, they have the opportunity to keep their data confidential F!'"mU<f  
for a specified period of time. This helps to allay concerns that the availability of their data in Gen- Z m>69gl  
Bank before publication may compromise their work. When the article containing the citation of the 6ZJQ '9f  
sequence or its Accession number is published, the sequence record is released. The database
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staff request that submitters notify GenBank of the date of publication so that the sequence can be I-I5^s  
released without delay. The request to release should be sent to gb-admin@ncbi.nlm.nih.gov. OYkd?L
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Direct Submissions a1&^P1.  
The typical GenBank submission consists of a single, contiguous stretch of DNA or RNA sequence *G38N]|u6  
with annotations. The annotations are meant to provide an adequate representation of the biological "
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information in the record. The GenBank Feature Table Definition [http://www.ncbi.nlm.nih.gov/col- EWi@1PAZK  
lab/FT/index.html] describes the various features and subsequent qualifiers agreed upon by the /:)4tIV  
International Nucleotide Sequence Database Collaboration. Y,r2m nq  
Currently, only nucleotide sequences are accepted for direct submission to GenBank. These }#1{GhsS  
include mRNA sequences with coding regions, fragments of genomic DNA with a single gene or >'eqOZM  
multiple genes, and ribosomal RNA gene clusters. If part of the nucleotide sequence encodes a VrG|/2  
1-2 6 s/O\A  
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NCBI Handbook GenBank 0ni5:t Yy  
protein, a conceptual translation, called a CDS (coding sequence), is annotated. The span of the [S%
 
CDS feature is mapped to the nucleotide sequence encoding the protein. A protein Accession num- _e W*  
ber (/protein_id) is assigned to the translation product, which will subsequently be added to the d:aQlW;}  
protein databases. +}!eAMQ  
Multiple sequences can be submitted together. Such batch submissions of non-related sequen- _<8y^y
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ces may be processed together but will be displayed in Entrez (Chapter 15) as single records. S;C3R5*:  
Alternatively, by using the Sequin submission tool (Chapter 12), a submitter can specify that several &N#)(rQ1  
sequences are biologically related. Such sequences are classified as environmental sample sets, }`X$ '  
population sets, phylogenetic sets, mutation sets, or segmented sets. Each sequence within a set 3y!CkJKv  
is assigned its own Accession number and can be viewed independently in Entrez. However, with (.cT<(TB  
the exception of segmented sets, each set is also indexed within the PopSet division of Entrez, thus hH\(>4l  
allowing scientists to view the relationship between the sequences. l40$}!!<  
What defines a set? Environmental sample, population, phylogenetic, and mutation sets all We`axkC  
contain a group of sequences that spans the same gene or region of the genome. Environmental mMR[(  
samples are derived from a group of unclassified or unknown organisms. A population set contains C<pF13*4  
sequences from different isolates of the same organism. A phylogenetic set contains sequences 0t~--/lA  
from different organisms that are used to determine the phylogenetic relationship between them. Hi9]M3Ub  
Sequencing multiple mutations within a single gene gives rise to a mutation set. hN.#ui5 $  
All sets, except segmented sets, may contain an alignment of the sequences within them and @1pdyKK  
might include external sequences already present in the database. In fact, the submitter can begin cIX59y#7  
with an existing alignment to create a submission to the database using the Sequin submission tool. f,$CiZ"  
Currently, Sequin accepts FASTA+GAP, PHYLIP, MACAW, NEXUS Interleaved, and NEXUS Con- 0Ec -/   
tiguous alignments. Submitted alignments will be displayed in the PopSet section of Entrez. h(Z7a%_  
Segmented sets are a collection of noncontiguous sequences that cover a specified genetic I|.B-$gH  
region. The most common example is a set of genomic sequences containing exons from a single a'|0e]  
gene where part or all of the intervening regions have not been sequenced. Each member record 67e1Y@Xu  
within the set contains the appropriate annotation, exon features in this case. However, the mRNA $6_J`7  
and CDS will be annotated as joined features across the individual records. Segmented sets them- YC$pT  
selves can be part of an environmental sample, population, phylogenetic, or mutation set.