Site Map
Guide to NCBI resources
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.
ProtEST
Protein
matches for ESTs
Retrovirus Resources
Enveloped RNA viruses
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
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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. |
 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. |
 Retrovirus Resources -
a collection of resources specifically designed to support the
research of retroviruses. Resources include a genotyping tool that
uses the BLAST algorithm to identify the genotype of a query
sequence; an alignment tool for global alignment of multiple
sequences; an HIV-1 automatic sequence annotation tool; and
annotated maps of 16 retroviruses viewable in GenBank, FASTA, and
graphic formats, with links to associated sequence records. |
 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. |
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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. |
 ProtEST - a tool that
presents a graphical view of matches between nucleotide sequences in
UniGene and possible translational products. To generate the
alignments, the 6-frame translations of mRNA and EST sequences in
UniGene are compared to protein sequences using BLASTX with -e 1e-6.
The translated nucleotide sequences are compared with proteins from
eight model organisms and the best match in each organism is
recorded. UniGene nucleotide sequences can thus have up to eight
matches in ProtEST. |
 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. |
| 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. |
Revised: June 9, 2005.
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