ABSTRACT
The GenBank sequence database continues to expand its data coverage, quality
control, annotation content and retrieval services. GenBank is comprised of DNA
sequences submitted directly by authors as well as sequences from the other
major public databases. An integrated retrieval system, known as Entrez,
contains data from GenBank and from the major protein sequence and structural
databases, as well as related MEDLINE abstracts. Users may access GenBank over
the Internet through the World Wide Web and through special client-server programs for text and sequence similarity searching. FTP, CD-ROM and e-mail servers are alternate means of access.
GenBank® (
1
) is the NIH's database of all publicly available nucleotide and protein
sequences including supporting bibliographic and biological information. Since
1992 it has been based at the National Center for Biotechnology Information
(NCBI), a division of the National Library of Medicine, located on the NIH
campus. NCBI was created by Congress in 1988 and specifically charged with
developing automated information systems to support molecular biology and
biotechnology. Its other mission is to conduct basic research and as part of
the NIH Intramural Program, NCBI scientists pursue research in genome analysis,
molecular structure modeling and prediction and mathematical methods for
sequence analysis.
NCBI builds GenBank primarily from the direct submission of sequence data from
authors and secondarily from scanning the journal literature. The data are
supplemented by incorporating sequences from other public databases. Through an
international collaboration with the EMBL Data Library in the UK and the DDBJ,
data are exchanged daily ensuring that each of these resources maintains a
comprehensive set of all known, public sequence information. The data are made
available at no cost through the Internet, either by downloading database files
or by text and sequence similarity search services.
GenBank has witnessed unprecedented growth over the past 12 months with more
sequence records added in this single period than in the entire previous 14
year history of GenBank. As of Release 90.0 in August, 1995, GenBank contained
over 353 713 490 nucleotide bases from 492 483 different sequences. Although
human entries predominate, constituting 54% of the total, >15 500 species are
represented. After
Homo sapiens
, the top four species in terms of bases include
Caenorhabditis elegans
,
Saccharomyces cerevisiae
,
Mus musculus
and
Arabidopsis thaliana
. Historically, the database has been doubling in size every 22 months, but that
rate has rapidly accelerated due to the enormous growth in data from expressed
sequence tags (ESTs). Over 56% of the sequences in the current release are ESTs
and most of the growth over the past year has come from the collaborative
project between Merck & Co. and Washington University (
2
).
Each GenBank entry includes a concise description of the sequence, the
scientific name and taxonomy of the source organism and a table of features
that identifies coding regions and other sites of biological significance, such
as transcription units, sites of mutations or modifications and repeats.
Protein translations for coding regions are included in the feature table.
Bibliographic references are included along with a link to the MEDLINE unique
identifier for all published sequences.
The files in the GenBank distribution have traditionally been divided into
`divisions' which roughly correspond to taxonomic divisions, for example
bacteria, viruses, primates, rodents, etc. In recent years, divisions have been
added for patent sequences, ESTs and sequence tagged sites (STSs). The patent
sequences are from the US Patent and Trademark Office and from the European
Patent Office and are being entered into the database as part of an ongoing
cooperative project among the US, European and Japanese patent offices and the
sequence databases.
A new genomes division will be created for the placement of chromosome- or genome-length sequences. The need for such a division arises from the
production of sequences >350 000 bases, the upper limit for single database
entries. Submitters of large entries are being encouraged to create multiple
records of <350 kb, corresponding to the natural units in which the sequencing was done,
often cosmid-size pieces or entries containing only a few genes. The genomes division
will contain virtual records whose feature tables will specify how to assemble
the individual entries into a single large, contiguous sequence. Thus,
retrieval software will be able to provide customized views on demand of the
complete genome, chromosome or subregion of interest.
ESTs are the most rapidly-expanding source of new genes. Last year there were 50 214 sequences in
the EST Division of GenBank (dbEST) with 45% of these derived from human
tissues (
3
). Currently dbEST contains 328 905 sequences with 80% coming from ~50 different human tissues or cell types. The remaining 20% are derived
from 43 other organisms with
Arabidopsis thaliana
(21 056),
Caenorhabditis elegans
(12 102) and
Oryza sativa
(11 015) being abundantly represented by >10 000 ESTs each. Of the 262 108
human ESTs currently in dbEST, 185 480 (71%) have been contributed by the
Washington University-Merck & Co. project. There have been >200 000 queries of dbEST data to date,
including BLAST searches, e-mail retrievals, WWW accesses and anonymous FTP downloads. dbEST data
assisted in the identification of a gene for familial Alzheimer's disease (
4
). In fact, 78% of the 45 human disease genes isolated by positional cloning to
date, have at least one exact match to ESTs in dbEST (
5
). An international consortium is converting ESTs into gene-based STSs to develop transcript maps of the human genome (
6
). dbEST sequences can be searched by the BLAST e-mail server and full reports of EST records can be obtained by querying
the NCBI e-mail server (retrieve{at}ncbi.nlm.nih.gov). Summary information on dbEST and
a query capability are available through the NCBI WWW home page listed above.
The dbSTS continues to expand rapidly. The most notable development of the past
year is the availability of ~2000 gene-based STSs derived from ESTs and mapped on human genomic DNA cloned
in YAC libraries by the Whitehead/MIT genome center by T. Hudson and
colleagues. This laboratory is part of an international consortium that is
developing transcript maps of the human genome (
6
). In addition to YAC maps, a major goal of the project is to create high-resolution radiation hybrid maps of human chromosomes. dbSTS contains PCR
primers, reaction conditions and map locations for gene-based markers derived from this project. Such data will be used to support
the visualization of transcript maps in the new genomes division of GenBank.
The data in GenBank come from two primary sources: (i) authors who submit data
directly to the collaborating databases; and (ii) annotators at NCBI who
extract the information from relevant journals. Data are exchanged daily with
collaborating databases so that the daily updates from NCBI servers incorporate
the most recently available sequence data from all sources.
The majority of entries continue to enter the database through direct author
submission. Many journals have the policy of requiring authors with sequence
data to submit data directly to the database as a condition of publication.
Even for those journals without a mandatory submission policy, author
submission has the positive benefits of acquiring annotation information
directly from the authors and reducing the time-lag between publication and the appearance of the sequence in the
database.
In early 1996, funding agencies in the US, Europe and Japan will begin to
support pilot sequencing projects with the goal of producing tens to hundreds
of megabases of human genomic DNA sequence over the next 1-3 years. NCBI will be working closely with a number of centers performing
this work to ensure timely incorporation of these data for public release. In
parallel, NCBI has developed methods to display these data integrated with
genetic and physical map data and to search the sequences more effectively
(e.g. options in BLAST to mask Alu and other types of repetitive elements).
Already, GenBank offers special batch procedures for large-scale sequencing groups to facilitate data submission.
Most individual submissions are now received through a Web-based data submission tool, BankIt. With BankIt, authors enter sequence
information directly into a form, edit as necessary and add biological
annotation (e.g. coding regions, mRNA features). Free-form text boxes provide the option of using your own words to describe the
sequence, without having to learn formatting rules or use restricted
vocabularies. BankIt creates a draft record in GenBank flat file format for the
user to review and revise. A standalone program for Macintoshes and PCs is also
available at no charge. It can be obtained by anonymous FTP to
`ncbi.nlm.nih.gov' in the `pub/authorin' directory or by a phone or e-mail (authorin{at}ncbi.nlm.nih.gov) request. Once a submission is completed,
users can e-mail it to the address: `gb-sub{at}ncbi.nlm.nih.gov'.
GenBank staff can usually assign an author an accession number within 1 working
day of receipt. The accession number serves as confirmation that the sequence
has been submitted and allows readers of the article to retrieve the relevant
data. All direct submissions receive a systematic quality assurance review
including screening against GenBank to identify full or partial matches,
checking for vector sequence and verifying proper translation of coding
regions. A draft of the GenBank record is passed back to the author for review
before entering the database. Authors have the right to request that their
sequence be kept confidential until the time of publication. In these cases,
authors are reminded to inform the database of the publication date in order to
have a timely release of the data. Although only the submitting scientist is
permitted to modify sequence data or annotations, all users are encouraged to
inform the database of possible errors or omissions using the e-mail address, `update{at}ncbi.nlm.nih.gov'.
GenBank is developing a platform-independent submission program called SEQUIN which will run stand-alone and over the network and will provide internal consistency
checks as well as access to feature validation tools so that the process of
sequence submission will not only be easier but will have the potential of
offering the author additional biological information about the sequence.
SEQUIN will be introduced in early 1996.
GenBank has a journal scanning operation to scan the current literature from
over 3500 journals and identify sequences which have been published but were
not submitted directly by authors. This operation has also proven successful in
updating publication information and in identifying sequences that had been
submitted confidentially and should be released.
In order to produce the GenBank database, NCBI maintains internally an
Integrated Database (ID) to track and index records from the multiple sources
of sequence data. These sources include submissions from EMBL, DDBJ, GDSB,
dbEST and patents plus amino acid sequences from PIR, SWISS-PROT, PRF and PDB. Integrated Database represents the most current view
that each data source has of its sequence data and allows NCBI to assign stable
identifiers (known as `gi identifiers' and which appear in the Comments and
Feature Table portion of GenBank entries). Through this approach, sequence
information from a wide variety of sources can have a uniform identification
system. These identifiers are stable and therefore help identify sequences
which have changed.
NCBI has begun producing a database of macromolecular 3-D structure information, specifically aimed at molecular modeling
research. MMDB is based upon the data in the Brookhaven Protein Data Bank
(PDB). By reorganizing and validating the PDB data, MMDB provides explicit
descriptions of a biopolymer's spatial structure, its chemical organization and
the linkage between the two. With MMDB, there is a clear cross-referencing between the 3-D structure and the chemistry of a macromolecule. Explicit linkages
have been made to the sequence entries within the ID database so that, with the
appropriate graphics software, users are able to view the 3-D structure of proteins identified via text or similarity searching of the
sequence database.
Entrez is an integrated database retrieval system which accesses DNA and protein
sequence data, related MEDLINE references, a collection of genome data and 3-D structures from MMDB (
7
). The DNA and protein sequence data are integrated from a variety of sources,
including GenBank, EMBL, DDBJ, dbEST, dbSTS, GSDB, PIR, SWISS-PROT, Protein Research Foundation (PRF), PDB and patents. The MEDLINE
references are papers indexed under the NLM's Medical Subject Heading (MeSH),
`genetic'. The genome dataset includes information on the large-scale organization of completely sequenced chromosomes or genomes, such as
physical and genetic maps and aligned sequences.
The linkages among data sources are shown in Figure
1
. The DNA sequence, protein sequence, MEDLINE, genome and 3-D structure data are linked to provide easy traversal among the datasets.
Entrez provides an entry point into sequence or bibliographic records by simple
Boolean queries. From the record, hypertext links may be used to navigate
through the information space using a point-and-click interface. Some of the links are simple cross-references, for example, between a sequence and the abstract
of the paper in which the sequence was reported or between a protein sequence
and its corresponding DNA sequence. Other links, however, are based on computed
similarities among the sequences or among the textual documents. The
precomputed neighbors allow very rapid access for browsing groups of related
records.
One of the most common uses of GenBank is sequence similarity searching. NCBI
offers the BLAST family of search programs to perform fast searching with
rigorous statistical methods for judging the significance of matches. NCBI
offers client programs for executing BLAST (
8
,
9
) queries directly over the Internet. Information on registering hosts for BLAST
clients and obtaining software can be obtained by e-mail to the address: `blast-help@ncbi.nlm.nih.gov'. World Wide Web access is also available for
BLAST searching.
Users on the Internet can use the ftp program to download the entire GenBank
release or the daily updates (which also incorporate sequence data from other
public databases). Files of the full release and daily updates of the GenBank
database are available for anonymous ftp from `ncbi.nlm.nih.gov' (130.14.25.1).
The full release in flat-file format is available as compressed files in the directory, `genbank'.
A cumulative update file is contained in the sub-directory, `daily' and a non-cumulative set of updates is in the sub-directory, `daily-nc'. ASN.1 formatted data are in the directory, `ncbi-asn1'. Software tools for handling the ASN.1 data
and for developing ASN.1 applications can be found in the directory
`toolbox/ncbi_tools'.
Users with access to electronic mail can search GenBank and 10 other databases
by accession number or Boolean combinations of text words. To start, send a
mail message containing the word `help' to: `retrieve@ncbi.nlm.nih.gov'. BLAST
sequence similarity searching is also available via e-mail through the address: `blast{at}ncbi.nlm.nih.gov'.
GenBank data are available on CD-ROM through a subscription service with the Government Printing Office
(Tel: +1 202 783 3238, FAX: +1 202 512 2233). Order forms are also included in
each issue of NCBI News, a free subscription to which may be obtained by
contacting NCBI. A new release of the database appears every 2 months. Each
release contains a new, full copy of the database and is available in the
following two versions.
The Flat File version provides the same flat file format in which GenBank has
been distributed for many years. Each release is a full release incorporating
all previous GenBank data supplemented by new data from direct submissions,
NCBI journal scanning, patents and the other sequence databases. Conceptual
translations of coding regions appear in feature tables. The release contains
the standard index files and is organized into divisions. No retrieval software
is provided. The distribution currently requires two CD-ROMs.
The GenBank Fellowship Program is a new NCBI initiative to improve the quality
of the database and also to serve as a bioinformatics training program. GenBank
fellows are selected for strong backgrounds in biology and for a motivation to
apply computational tools to the organization of electronic data in molecular
and structural biology, genetics and phylogeny. Training is provided in the
Unix operating system, software tools for manipulating data, files and
processes, sequence analysis methods and statistics and database management
systems. GenBank fellows, under the supervision of a mentor from NCBI's
Computational Biology Branch, pursue various applied research projects to
improve the quality and annotation of GenBank entries, to reduce sequence
redundancy and to establish and maintain links to other databases such as those
containing genetic and physical mapping data and 3-D macromolecular structures. Currently five GenBank fellows are in the
program and applications are reviewed on a continuing cycle.
GenBank, National Center for Biotechnology Information, Building 38A, Room 8S-803, 8600 Rockville Pike, Bethesda, MD 20894, USA. Tel: +1 301 496 2475;
Fax: +1 301 480 9241.
http://www.ncbi.nlm.nih.gov/, NCBI World Wide Web Home Page.
gb-sub@ncbi.nlm.nih.gov, Submission of sequence data to GenBank.
update@ncbi.nlm.nih.gov, Revisions to GenBank entries and notification of
release of `hold until published' entries.
info{at}ncbi.nlm.nih.gov, General information about NCBI and GenBank services.
If you use GenBank as a tool in your published research, we ask that this paper
be cited.
REFERENCES
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