Entrez Bioinformatics Databases and Tools : Tools

This library guide is designed by Lyra Eugenio-Thomson to assist in the use of bioinformatics databases and tools from Entrez, a retrieval system of the National Center for Biotechnology Information (NCBI).

Similarity Searching

BLAST
BLAST finds regions of similarity between biological sequences.
HELP

Nucleotide Sequence Analysis

BLAST
BLAST finds regions of similarity between biological sequences.
HELP
Electronic PCR
Identifies sequence tagged sites(STSs)within DNA sequences.
Gene
Searchable database of genes, from RefSeq genomes, and defined by sequence and/or located in the NCBI Map Viewer.
Model Maker
View the evidence that was used to build a gene model on assembled genomic sequence, and to create your own version of the model by selecting exons of interest.
MAP VIEWER HELP
ORF Finder
Graphical analysis tool which finds all open reading frames of a selectable minimum size in a user's sequence or in a sequence already in the database.
Organism Specific Resources
Contains links to organism-specific resources.
SAGEmap
Serial analysis of gene expression (SAGE) data repository supporting public use and dissemination of SAGE data
[SITE CURRENTLY UNAVAILABLE: SAGEmap is undergoing restructuring and revised tag to gene mappings].
Spidey
An mRNA-to-genomic alignment program.
FAQ
Splign
Utility for computing cDNA-to-Genomic, or spliced sequence alignments.
DOCUMENTATION
VecScreen
System for quickly identifying segments of a nucleic acid sequence that may be of vector origin.
OVERVIEW
Viral Genotyping Tool
Tool helps identify the genotype of a viral sequence.
HELP

Protein Sequence Analysis and Proteomics

BLAST
BLAST finds regions of similarity between biological sequences.
HELP
BLink
BLink ("BLAST Link") displays the results of BLAST searches that have been done for every protein sequence in the Entrez Proteins data domain.

To access it, follow the BLink link displayed beside any hit in the results of an Entrez Proteins search.
CD Search
Searches the Conserved Domain Database with Reverse Position Specific BLAST.
HELP
CDART
Displays the functional domains that make up the protein and lists proteins with similar domain architectures when given a protein query sequence.
HELP
TaxPlot
Tool for 3-way comparisons of genomes on the basis of the protein sequences they encode.

Molecular Structure Analysis

Cn3D
Helper application for your web browser that allows you to view 3-dimensional structures from NCBI's Entrez retrieval service.
TUTORIAL
FAQ
VAST Search
Compares 3D coordinates of a newly determined protein structure to those in the MMDB/PDB database.
HELP
SEARCH HELP
CD Search
Searches the Conserved Domain Database with Reverse Position Specific BLAST.
HELP

Quick Links for Tools

Go directly to the major Entrez data analysis tools.

Genome Analysis

Entrez Genome
Search whole genomes of over 1000 viruses & over 100 microbes.
HELP
COGs (Clusters of Orthologous Groups)
Phylogenetic classification of proteins encoded in complete genomes.
Map Viewer
Shows integrated views of chromosome maps for many organisms, including human and numerous other vertebrates, invertebrates, fungi, protozoa, and plants.
HELP
SKY/M-FISH and CGH Database
Provides a public platform for investigators to share and compare their molecular cytogenetic data.
HELP

Gene Expression

GEO (Gene Expression Omnibus)
A public functional genomics data repository supporting MIAME-compliant data submissions.
FAQ
SAGEmap
Serial analysis of gene expression (SAGE) data repository supporting public use and dissemination of SAGE data
[SITE CURRENTLY UNAVAILABLE: SAGEmap is undergoing restructuring and revised tag to gene mappings].
CGAP (Cancer Genome Anatomy Project)
Project goal of CGAP is to determine the gene expression profiles of normal, precancer, and cancer cells, leading eventually to improved detection, diagnosis, and treatment for the patient.
EDUCATIONAL RESOURCES
UniGene DDD
An online tool to compare computed gene expression profiles between selected cDNA libraries.
QUERY TIPS
FAQ