Site Map
Guide to NCBI resources
Tools for Programmers
BLAST
Standard tool for sequence analysis
BLink
BLAST Link
CDART
Conserved
Domain Architecture Retrieval Tool
CD search
Conserved
Domain Database search
CGAP
Cancer Gene Anatomy Project
Cn3D
View 3-dimensional structures
COGs
Clusters of Orthologous Groups
Electronic PCR
Compare your sequence to COG database
Entrez Gene
Gene-based view of the data from a wide range of genomes
Entrez Genomes
Whole genomes of over 1000 organisms
GEO
Gene Expression Ominibus
Map Viewer
Interactive chromosome viewer
Model Maker
View evidence used to build a gene model
ORF finder
Open reading frames
Organism Specific Resources
Bee, Cat, Chicken, Cow, etc.
SAGEmap
Serial Analysis of Gene Expression Tag
to Gene Mapping
Sequin
A DNA Sequence Submission and Update Tool
SKY/M-FISH
& CGH Database
Share and compare molecular
cytogenetic data
VAST search
Structure similarity search
VecScreen
Vector contamination identifier
TaxPlot
Protein homologs in Complete Microbial / Eukaryotic genomes
UniGene DDD
Gene-oriented clusters
Viral Genotyping Tool
Determine the genotypes of recombinant or non-recombinant viral nucleotide sequences
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 The
Basic Local Alignment Search Tool (BLAST)
for comparing gene and protein sequences against others in public
databases, now comes in several types including PSI-BLAST, PHI-BLAST,
and BLAST 2 sequences. Specialized BLASTs are also available for human,
microbial, malaria, and other genomes, as well as for vector contamination,
immunoglobulins, and tentative human consensus sequences. |
 Electronic
PCR - allows you to search your DNA sequence for sequence tagged
sites (STSs) that have been used as landmarks in various types of
genomic maps. It compares the query sequence against data in NCBI's UniSTS, a unified, non-redundant view of STSs from a wide range of sources.
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 Entrez
Gene - each Entrez Gene record encapsulates a wide range of information
for a given gene and organism. When possible, the information includes
results of analyses that have been done on the sequence data. The
amount and type of information presented depend on what is available
for a particular gene and organism and can include: (1) graphic summary
of the genomic context, intron/exon structure, and flanking genes,
(2) link to a graphic view of the mRNA sequence, which in turn shows
biological features such as CDS, SNPs, etc., (3) links to gene ontology
and phenotypic information, (4) links to corresponding protein sequence
data and conserved domains, (5) links to related resources, such as
mutation databases. Entrez Gene is a successor to LocusLink.
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 Model
Maker - allows you to view the evidence (mRNAs, ESTs, and gene
predictions) that was aligned to assembled genomic sequence to build
a gene model and to edit the model by selecting or removing putative
exons. You can then view the mRNA sequence and potential ORFs for
the edited model and save the mRNA sequence data for use in other
programs. Model Maker is accessible from sequence maps that were analyzed
at NCBI and displayed in Map Viewer. |
 ORF
Finder - identifies all possible ORFs in a DNA sequence by locating
the standard and alternative stop and start codons. The deduced amino
acid sequences can then be used to BLAST against GenBank. ORF finder
is also packaged in the sequence submission software Sequin. |
 Organism
Specific Resources - Bee, Cat, Chicken, Cow, etc. |
 SAGEmap
- provides a tool for performing statistical tests designed specifically
for differential-type analyses of SAGE (Serial Analysis of Gene Expression)
data. The data include SAGE libraries generated by individual labs
as well as those generated by the Cancer Genome Anatomy Project (CGAP),
which have been submitted to Gene Expression Omnibus (GEO). Gene expression
profiles that compare the expression in different SAGE libraries are
also available on the Entrez GEO Profiles pages. It is possible to
enter a query sequence in the SAGEmap resource to determine what SAGE
tags are in the sequence, then map to associated SAGEtag records and
view the expression of those tags in different CGAP SAGE libraries. |
 Spidey
- aligns one or more mRNA sequences to a single genomic sequence.
Spidey will try to determine the exon/intron structure, returning
one or more models of the genomic structure, including the genomic/mRNA
alignments for each exon. |
 Splign
- is a utility for computing cDNA-to-Genomic alignments based on a variation of the Needleman-Wunsch algorithm combined with Blast for compartment detection and greater performance. |
 VecScreen
- a tool for identifying segments of a nucleic acid sequence that
may be of vector, linker, or adapter origin prior to sequence analysis
or submission. VecScreen was developed to combat the problem of vector
contamination in public sequence databases. |
 Viral Genotyping Tool - a web-based program that identifies the genotype (or
subtype) of recombinant or non-recombinant viral nucleotide sequences.
It works by using BLAST to compare a query sequence to a set of reference sequences for known genotypes. Predefined reference genotypes exist for three major viral pathogens: human immunodeficiency virus 1 (HIV-1), hepatitis C virus (HCV) and hepatitis B virus (HBV), as well as for poliovirus. User-defined reference sequences can be used at the same time. The query sequence is broken into segments for comparison to the reference so that the mosaic organization of recombinant sequences is revealed. The results are displayed graphically using color-coded genotypes. Therefore, the genotype(s) of any portion of the query can quickly be determined. |
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| The
Basic Local Alignment Search Tool (BLAST)
for comparing gene and protein sequences against others in public
databases, now comes in several types including PSI-BLAST, PHI-BLAST,
and BLAST 2 sequences. Specialized BLASTs are also available for human,
microbial, malaria, and other genomes, as well as for vector contamination,
immunoglobulins, and tentative human consensus sequences. |
 BLink
- ("BLAST Link") displays the
results of BLAST searches that have been done for every protein sequence
in the Entrez Proteins data domain. |
 CD
Search - search the Conserved Domain Database with Reverse Position
Specific BLAST. |
 CDART
- when given a protein query sequence, CDART displays the functional
domains that make up the protein and lists proteins with similar domain
architectures. |
Open Mass Spectrometry Search Algorithm (OMSSA) - The OMSSA search service allows
proteomics researchers to submit the mass spectra of peptides and proteins for identification.
OMSSA then compares these mass spectra to theoretical ions generated from data
libraries of known protein sequences and ranks the results using a score
derived from classical hypothesis testing. |
 TaxPlot
- a tool for 3-way comparisons of genomes on the basis of the
protein sequences they encode. To use TaxPlot, one selects a reference
genome to which two other genomes are compared. Pre-computed BLAST
results are then used to plot a point for each predicted protein in
the reference genome, based on the best alignment with proteins in
each of the two genomes being compared. |
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 Cn3D
- Cn3D is a helper application for your web browser that allows you
to view 3-dimensional structures from NCBI's Entrez retrieval service.
Cn3D runs on Windows, Macintosh, and Unix. |
 VAST
Search - VAST Search is NCBI's
structure-structure similarity search service. It compares 3D coordinates
of a newly determined protein structure to those in the MMDB/PDB database.
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| CD
Search - search the Conserved Domain Database with Reverse Position
Specific BLAST. |
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 Entrez
Genomes - whole genomes of over 1000 organisms. The genomes represent
both completely sequenced organisms and those for which sequencing
is in progress. All three main domains of life - bacteria, archaea,
and eukaryota - are represented, as well as many viruses, phages,
viroids, plasmids, and organelles.. Entrez Genomes provides graphical
overviews of complete genomes/chromosomes and the ability to explore
regions of interest in progressively greater detail. |
 COGs
- Clusters of Orthologous Groups - a natural system of gene families
from complete genomes. Clusters of Orthologous Groups (COGs) were
delineated by comparing protein sequences encoded in 43 complete genomes,
representing 30 major phylogenetic lineages. Each COG consists of
individual proteins or groups of paralogs from at least 3 lineages
and thus corresponds to an ancient conserved domain. |
 Map
Viewer - shows integrated views of chromosome maps for
many organisms, including human and numerous other vertebrates, invertebrates, fungi, protozoa,
and plants. Map Viewer is used to view assembled genomes (either draft or complete) and is a
valuable tool for the identification and localization of genes and other biological features.
Multiple map displays are aligned based on shared marker and gene names when available, and
sequence map displays are based on a common sequence coordinate system. Sequence data for
chromosome regions of interest can be downloaded, biological annotations can be viewed in graphical
format and/or downloaded in tabular format, and gene models can be manipulated in the associated
ModelMaker tool. |
 SKY/M-FISH
& CGH Database - The NCI and NCBI SKY/M-FISH and CGH Database
is a repository of publicly submitted data from Spectral Karyotyping
(SKY), Multiplex Fluorescence In Situ Hybridization (M-FISH), and
Comparative Genomic Hybridization (CGH), which are complementary fluorescent
molecular cytogenetic techniques. SKY/M-FISH permits the simultaneous
visualization of each human or mouse chromosome in a different color,
facilitating the identification of chromosomal aberrations; CGH can
be used to generate a map of DNA copy number changes in tumor genomes.
Collaborative project with the National Cancer Institute. (
data submission instructions...) |
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 GEO
Gene Expression Omnibus - The Gene Expression Omnibus (GEO) provides
several tools to assist with the visualization and exploration of
GEO data. Datasets may be viewed as hierarchical cluster heat maps,
providing insight into the relationships between samples and co-regulated
genes. Individual gene expression profiles showing significant differences
between experimental subsets may be located using average subset rank
value comparisons. Related gene expression profiles may be identified
on the basis of sequence similarity, profile similarity, or homology.
Indicators of dataset normalization quality are provided as distribution
graphs, and by flagging outliers. Links to other NCBI sequence, mapping
and publication database resources are provided where possible. |
| SAGEmap
-provides a tool for performing statistical tests designed specifically
for differential-type analyses of SAGE (Serial Analysis of Gene Expression)
data. The data include SAGE libraries generated by individual labs
as well as those generated by the Cancer Genome Anatomy Project (CGAP),
which have been submitted to Gene Expression Omnibus (GEO). Gene expression
profiles that compare the expression in different SAGE libraries are
also available on the Entrez GEO Profiles pages. It is possible to
enter a query sequence in the SAGEmap resource to determine what SAGE
tags are in the sequence, then map to associated SAGEtag records and
view the expression of those tags in different CGAP SAGE libraries. |
 The
Cancer Genome Anatomy Project (CGAP)
- aims to decipher the molecular anatomy of cancer cells. CGAP develops
profiles of cancer cells by comparing gene expression in normal, precancerous,
and malignant cells from a wide variety of tissues. |
 UniGene
DDD - Digital Differential Display - an online tool to compare
computed gene expression profiles between selected cDNA libraries.
Using a statistical test, genes whose expression levels differ significantly
from one tissue to the next are identified and shown to the user.
Additional information about UniGene is above, including a list of
organisms represented. |
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Entrez Programming Utilities - E-Utilities are a set of programs that
provide a stable interface into the Entrez retrieval system. The eUtils use
a fixed URL syntax that translates a standard set of input parameters into values
necessary for various NCBI software components to search for and retrieve data from
23 Entrez databases. |
Information Engingeering Branch - IEB is responsible for developing NCBI's
resources and databases. Access is provided to documentation, access to NCBI
software tools and libraries, and announcements. |
Revised: September 28, 2007.
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