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Nucleic Acids Res. 2001 January 1; 29(1): 11–16. | PMCID: PMC29800 |
Database resources of the National
Center for Biotechnology Information David L. Wheeler,a Deanna
M. Church, Alex
E. Lash, Detlef
D. Leipe, Thomas
L. Madden, Joan
U. Pontius, Gregory
D. Schuler, Lynn
M. Schriml, Tatiana
A. Tatusova, Lukas Wagner, and Barbara
A. Rapp National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA Received October 3, 2000; Accepted October 4, 2000. In addition to maintaining the GenBank® nucleic acid sequence
database, the National Center for Biotechnology Information (NCBI)
provides data analysis and retrieval resources that operate on the
data in GenBank and a variety of other biological data made available
through NCBI’s Web site. NCBI data retrieval resources
include Entrez, PubMed, LocusLink and the Taxonomy Browser. Data
analysis resources include BLAST, Electronic PCR, OrfFinder, RefSeq,
UniGene, HomoloGene, Database of Single Nucleotide Polymorphisms
(dbSNP), Human Genome Sequencing, Human MapViewer, GeneMap’99,
Human–Mouse Homology Map, Cancer Chromosome Aberration
Project (CCAP), Entrez Genomes, Clusters of Orthologous Groups (COGs) database,
Retroviral Genotyping Tools, Cancer Genome Anatomy Project (CGAP),
SAGEmap, Gene Expression Omnibus (GEO), Online Mendelian Inheritance
in Man (OMIM), the Molecular Modeling Database (MMDB) and the Conserved
Domain Database (CDD). Augmenting many of the Web applications are
custom implementations of the BLAST program optimized to search
specialized data sets. All of the resources can be accessed through
the NCBI home page at: http://www.ncbi.nlm.nih.gov. The National Center for Biotechnology Information (NCBI) at the
National Institutes of Health was created in 1988 to develop information
systems for molecular biology. In addition to maintaining the GenBank® ( 1) nucleic acid sequence database, to which
data is submitted directly by the scientific community, NCBI provides
data retrieval systems and computational resources for the analysis
of GenBank data and the variety of other biological data made available
through NCBI. The data accessible from NCBI’s home page ( http://www.ncbi.nlm.nih.gov)
runs the gamut from short sequences representative of parts of genes
to complete genomes, protein structures and clinical descriptions
of genetic disorders. NCBI offers an array of computational resources
to aid in the analysis of each type of data. For this overview,
the NCBI suite of database resources is grouped into seven categories:
database retrieval systems, sequence similarity search programs, resources
for analysis of gene-level sequences, resources for chromosomal
sequences, resources for genome-scale analysis, resources for the
analysis of gene expression and phenotypes, and resources for protein
structure and modeling. Table 1 provides
an at-a-glance summary of these resources. | Table 1. A summary of selected web-based data resources, in addition
to GenBank, provided by NCBI |
Entrez Entrez ( 2) is an integrated
database retrieval system that accesses DNA and protein sequences,
genome maps, population sets, protein structures from MMDB ( 3) and the biomedical literature via PubMed
and Online Mendelian Inheritance in Man (OMIM), with embedded links
to the NCBI taxonomy. The sequences in Entrez, especially protein
sequences, are obtained from a variety of database sources [including GenBank
protein translations, Protein Identification Resource ( 4), SWISS-PROT ( 5),
Protein Research Foundation, Protein Data Bank ( 6)
and RefSeq ( 7)], and
therefore include more sequence data than GenBank alone. PubMed
includes primarily the 10.7 million references and abstracts in
MEDLINE®, with links to the full-text of more than 1100
journals available on the Web. Entrez provides text searching of sequence or bibliographic records
using simple Boolean queries, plus extensive links to related information.
Some links are simple cross-references, for example, from a sequence
to the abstract of the paper in which it was reported, from a protein
sequence to its corresponding DNA sequence, or to alignments with
other sequences. Other links are based on computed similarities
among the sequences or MEDLINE abstracts. These pre-computed ‘neighbors’ allow
rapid access for browsing groups of related records. A service called
LinkOut expands the range of external links from individual database
records to related outside services, including organism-specific
genome databases. The Taxonomy Browser The NCBI taxonomy database indexes over 79 000 organisms that
are represented in the sequence databases with at least one nucleotide
or protein sequence. The Taxonomy Browser can be used to view the
taxonomic position or retrieve sequence and structural data for
a particular organism or group of organisms. Searches of the NCBI
taxonomy may be made on the basis of whole, partial or phonetically-spelled
organism names, and direct links to organisms commonly used in biological
research are also provided. The new Entrez Taxonomy system adds
the ability to display custom taxonomic trees representing user-defined
subsets of the full NCBI taxonomy. LocusLink The LocusLink database of official gene names and other gene identifiers,
described elsewhere in this issue ( 7),
was developed at NCBI in conjunction with several international
collaborators, and offers a single query interface to curated sequences
and descriptive information about genes. THE BLAST FAMILY OF SEQUENCE-SIMILARITY SEARCH PROGRAMS The BLAST family of search programs ( 8, 9) is provided for the most frequent type
of analysis performed on GenBank, the sequence-similarity search.
NCBI’s Web interface to the standard BLAST 2.1 program
accepts either a sequence or accession number and performs the search
using either an identity matrix for blastn (nucleotide) searches
or a PAM or BLOSUM scoring matrix for protein searches. BLAST produces
a set of gapped alignments, with links to the full document records,
accompanied by an alignment score and a measure of statistical significance,
called the Expectation Value, for judging the quality of the alignment.
Web BLAST provides a graphical overview of the alignments, color-coded by
alignment score, which clearly shows the extent and quality of sequence
similarities, as well as the disposition of gaps in the alignments.
Web BLAST can also generate a taxonomically organized output that
emphasizes taxonomic patterns of sequence-similarity. The default databases searched by BLAST are the non-redundant
(nr) nucleotide and protein databases constructed from the Entrez
databases. Several specialized databases may also be searched, and
searches may be restricted to sequences from a particular organism.
Query sequences may be filtered for low complexity or human repeats.
Customized BLAST pages allow queries against finished human genomic
data, microbial genomes or the genomes of malaria-associated pathogens. Specialized versions of BLAST are offered for the needs of protein
similarity searching. Position Specific Iterated BLAST (PSI-BLAST)
( 9) initially performs a conventional
BLAST search to produce alignments from which it constructs a position
specific score matrix (PSSM). Subsequent BLAST iterations use this
PSSM to find similarities in the database. Pattern Hit Initiated
BLAST (PHI-BLAST) ( 10) requires
both a query sequence and a pattern present within the query sequence. The
pattern specifies an obligatory match between query and database
sequences, about which optimal local alignments are constructed.
Another variant, ‘BLAST2Sequences’ ( 11), compares
two DNA or protein sequences and produces a dot-plot representation
of the alignments it reports. Basic BLAST 2.0 searches can also be performed by email through
the address: blast/at/ncbi.nlm.nih.gov. Documentation can
be obtained by sending the word ‘help’ to the
server address. RESOURCES FOR GENE-LEVEL SEQUENCES UniGene To manage the redundancy of the EST data, NCBI has developed UniGene
( 12), a system for automatically
partitioning GenBank sequences, including ESTs, into a non-redundant
set of gene-oriented clusters. There are currently five UniGene databases;
for human, mouse, rat, zebrafish and cow. UniGene starts with entries
in the appropriate organismic division of GenBank, combines these
with ESTs of that organism and creates clusters of sequences that
share virtually identical 3′ untranslated
regions (3′ UTRs). Each UniGene cluster
contains sequences that represent a unique gene, and is linked to
related information, such as the tissue types in which the gene
is expressed, model organism protein similarities, the LocusLink report
for the gene and its map location. In the human UniGene database,
over 1.8 million human ESTs in GenBank have been reduced 21-fold
in number to approximately 84 000 sequence clusters. In a similar
fashion, the mouse, rat, zebrafish, and cow ESTs have been organized
as 73 000, 37 000, 10 000, and 5500 clusters, respectively. The
human UniGene collection has been effectively used as a source of
mapping candidates for the construction of a human gene map ( 13). In this case, the 3′ UTRs
of genes and ESTs are converted to sequence-tagged sites (STSs)
that are then placed on physical maps and integrated with pre-existing
genetic maps of the genome. The UniGene collection has also been
used as a source of unique sequences for the fabrication of ‘chips’ for
the large-scale study of gene expression ( 14).
UniGene databases are updated weekly with new EST sequences, and
bimonthly with newly characterized sequences. UniGene clusters may
be searched in several ways; by gene name, chromosomal location,
cDNA library, accession number, and ordinary text words. Cluster sequences
may also be downloaded by FTP. HomoloGene HomoloGene is a database of both curated and calculated orthologs
and homologs for the human, mouse, rat, zebrafish and cow genes
represented in UniGene and LocusLink. Curated orthologs include
gene pairs from the Mouse Genome Database (MGD) at the Jackson Laboratory,
the Zebrafish Information (ZFIN) database at the University of Oregon
and from published reports. Computed orthologs and homologs, which
are considered putative, are identified from BLAST nucleotide sequence
comparisons between all UniGene clusters for each pair of organisms.
HomoloGene also contains a set of triplet ortholog clusters in which
orthologous clusters in two organisms are both orthologous to the
same cluster in a third organism. For the three organisms human,
mouse and rat, there are currently over 7000 of these self-consistent
triplets. The HomoloGene database can be queried using UniGene ClusterIDs,
LocusLink LocusIDs, gene symbols, gene names and nucleotide accession
numbers, as well as those terms in UniGene cluster titles. The current
datasets for the calculated orthologs and homologs and the Mutually
Orthologous Pairs are also available via FTP. RefSeq The References Sequence (RefSeq) database, described elsewhere
in this issue ( 7), provides curated
reference sequences for mRNAs and proteins from human and other
organisms. A database of Single Nucleotide Polymorphisms (dbSNP) The database of Single Nucleotide Polymorphisms (dbSNP), described
elsewhere in this issue ( 15),
serves as a repository for both single base nucleotide substitutions
and short deletion and insertion polymorphisms that are deposited
by the research community. ORF Finder ORF Finder performs a six-frame translation of a nucleotide query
and returns a graphic that indicates the location of each open reading
frame (ORF) found. Restrictions on the size of the ORFs returned
may be set by the user. The sequences of predicted protein products
can be submitted directly for BLAST similarity searching or searching
against the COGs (see below) database. Electronic PCR PCR-based assays for STSs can be used for gene identification and
mapping. Electronic PCR (e-PCR) is a tool for locating STSs within
a nucleotide sequence by comparing the query against the dbSTS database
of STS sequences and primer pairs. The e-PCR application accepts
either an accession number or sequence as input, and returns a table
of links to matching dbSTS records as well as the primer pairs used
to amplify each STS identified. RESOURCES FOR CHROMOSOMAL SEQUENCES Human Genome Sequencing The Human Genome Sequencing ( 16)
site shows chromosome-specific progress of the human sequencing
project, provides access to individual contigs and assemblies, and offers
chromosome-specific BLAST searches. Links to contributing genome
sequencing centers are also provided. Sequence data may be downloaded
by contig or chromosome. Human Genome MapViewer The Human Genome MapViewer can display the human genome data
using up seven parallel chromosomal maps simultaneously. The maps
displayed can be selected from a set of 19, and include cytogenetic
maps, such as chromosomal ideograms, sequence-based maps, such as
those showing contigs, genes, and SNPs, and radiation hybrid maps,
such as the G3 and GB4 maps used to construct GeneMap ’99.
Queries against the entire human genome or particular chromosomes can
be made using gene names or symbols, marker names, SNP identifiers,
accession numbers and other identifiers. The Human Genome MapViewer
is tightly integrated with other NCBI databases such as LocusLink
and dbSNP. A MapViewer similar to the Human Genome MapViewer is
also used to display the Drosophila genome data. GeneMap’99 An international consortium was formed in 1994 to construct a human
gene map by determining the locations of ESTs relative to a framework
of well-characterized genetic markers ( 17). The
current version of this map is the radiation hybrid map, GeneMap’99
( 13), featuring 30 261 unique
gene loci. The Human–Mouse Homology Maps, mouse sequencing resources The Human–Mouse Homology Maps are tables of genetic
loci in homologous segments of DNA from human and the mouse. The
map is computed by integrating orthologs curated by the Mouse Genome
Database with putative orthologs identified by homology. The maps
are linked to GeneMap’99, OMIM, LocusLink, dbSTS, BLAST2Sequences
and the Mouse Genome Database at The Jackson Laboratory. Other mouse genome
resources can be found on the Mouse Genome Sequencing page, analogous
to the Human Genome Sequencing page described above. The Cancer Chromosome Aberration Project (CCAP) The CCAP service is an initiative of the National Cancer Institute
(NCI) and NCBI. The data includes a compilation by F. Mitelman,
F. Mertens and B. Johansson of recurrent neoplasia-associated chromosomal
aberrations from the Cancer Chromosome Aberration Bank at the University
of Lund, Sweden ( 18). Also provided
are bacterial artificial chromosome (BAC) human chromosome mapping
data provided through CCAP’s fluorescent in
situ hybridization (FISH) effort. RESOURCES FOR GENOME-SCALE ANALYSIS Entrez Genomes The Entrez Genomes database ( 19)
provides access to genomic data contributed by the scientific community
for over 900 species whose sequencing and mapping is complete or
in progress, and now includes more than 30 complete microbial genomes.
Also included is a collection of 169 reference sequences for the complete
genomes of eukaryotic organelles. Data can be accessed hierarchically
starting from either an alphabetical listing or a phylogenetic tree
for complete genomes in each of six principle taxonomic groups.
One can follow the hierarchy to a graphical overview for the genome
of a single organism, on to the level of a single chromosome and,
finally, down to the level of a single gene. At each level are one or more views, pre-computed summaries and
links to analyses appropriate for that level. For instance, at the
level of a genome or a chromosome, a Coding Regions view displays
the location of each coding region, length of the product, GenBank
identification number for the protein sequence and name of the protein
product. An RNA Genes view lists the location and gene names for
ribosomal and transfer RNA genes. At the level of a single gene,
links are provided to pre-computed sequence neighbors for the gene product.
Any protein gene product that is a member of a COG ( 20) is
linked to the COGs database. A summary of COG functional groups
is also presented in tabular and graphical formats at the genome
level. For complete microbial genomes, pre-computed BLAST neighbors
for protein sequences, including their taxonomic distribution and
links to 3-D structures, are given in TaxTables and PDBTables, respectively.
Pairwise sequence alignments are presented graphically and linked
to the Cn3D macromolecular viewer ( 21),
which allows the interactive display of 3-D structures and sequence
alignments. Clusters of Orthologous Groups (COGs) The COGs database, described elsewhere in this issue ( 20), presents a compilation of orthologous
groups of proteins from completely sequenced organisms representing
phylogenetically distant clades. Retroviral genotyping tools Genotyping retrovirus sequences is important in the characterization
of viral genetic diversity, tracking of epidemics and vaccine development.
NCBI has developed a Web-based genotyping tool for the analysis
of retroviral genomes. The genotyping method employs a blastn comparison
between the retroviral sequence to be subtyped and a panel of reference sequences
provided by the user. An HIV-1-specific subtyping tool uses a set
of reference sequences taken from the principle HIV-1 variants. RESOURCES FOR THE ANALYSIS OF PATTERNS OF GENE EXPRESSION
AND PHENOTYPES The Cancer Genome Anatomy Project (CGAP) CGAP provides access to genetic data on normal, precancerous and
malignant cells generated by the NCI’s CGAP initiative. CGAP
cDNA library information may be retrieved by text words, gene name,
clone ID, tissue type, method of sample preparation, stage of tumor
development or by UniGene Cluster ID. Expression profiles of cDNA
libraries may be compared using either the Digital Differential
Display (DDD) tool or the xProfiler. CGAP also includes a directory
of tumor suppressor genes and oncogenes. SAGEmap Serial Analysis of Gene Expression (SAGE) refers to a technique
for taking a snapshot of the messenger RNA population of a cell
to obtain a quantitative measure of gene expression. NCBI’s
SAGEmap service implements many functions useful in the analysis
of SAGE data such as a two-way mapping between SAGE tag and UniGene.
SAGEmap can also construct a user-configurable table of data comparing
one group of SAGE libraries with another. Groups may be chosen for inclusion
in the table on the basis of several expression criteria specified
by the user. SAGEmap is updated weekly, immediately following the
update of UniGene. GEO The Gene Expression Omnibus (GEO) is an effort to build a data
repository and retrieval system for gene expression data derived
from any organism or artificial source. Gene expression data derived
from spotted microarray (microarray), high-density oligonucleotide
array (HDA), hybridization filter (filter) and serial analysis of
gene expression (SAGE) data, are being accepted. Online tools for
the interactive retrieval and analysis of this expression data are
under development. OMIM NCBI provides Web access to the OMIM database, a catalog of human
genes and genetic disorders authored and edited by Dr Victor A.
McKusick at The Johns Hopkins University ( 22). The
database contains information on disease phenotypes and genes, including
extensive descriptions, gene names, inheritance patterns, map locations
and gene polymorphisms. OMIM currently contains 11 925
entries, including data on 8594 established gene loci and 799 phenotypic
descriptions, and is now searchable using the powerful Entrez interface. THE MOLECULAR MODELING DATABASE THE CONSERVED DOMAIN DATABASE SEARCH Conserved domains are structural modules that have been re-used
frequently during the process of evolution. The Conserved Domain
Database (CDD) contains domains derived principally from two public
protein domain collections, the Simple Modular Architecture Research
Tool (Smart) ( 23), and Pfam ( 24). NCBI’s Conserved Domain
Search (CD-Search) service can be used to search a protein sequence
for conserved domains in the CDD. To produce the CDD a PSI-BLAST-type PSSM is calculated from
each domain alignment in the SMART and Pfam databases. These PSSMs
are then combined into a library that can be searched using Reverse
Position-Specific BLAST (RPS-BLAST), a BLAST variant that searches
a database of PSSMs with a protein sequence query. Wherever possible
CDD hits are linked to structures which, coupled with a multiple
sequence alignment of representatives of the domain hit, can be
viewed with NCBI’s 3-D molecular structure viewer, Cn3D
( 21). Most of the resources described here include documentation, other
explanatory material and references to collaborators and data sources
on the respective web sites. Several tutorials are also offered
under the Education link from NCBI’s home page. A Site
Map provides a comprehensive table of NCBI resources, and the What’s
New feature announces new and enhanced resources. Additional tools
to guide users to NCBI’s growing array of services are
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