Databases

E-Utilities Practical Guide
Written as part of the NCBI PowerScripting course, this manual describes the E-utilities from a practical standpoint and gives guidance on how to use the E-utilties to construct data download and analysis pipelines. The manual can be searched online or downloaded in PDF format
NCBI C++ Toolkit Manual
A comprehensive manual on the NCBI C++ toolkit, including its design and development framework, a C++ library reference, software examples and demos, FAQs and release notes. The manual is searchable online and can be downloaded as a series of PDF documents.
NCBI Glossary
Part of the NCBI Handbook, this glossary contains descriptions of NCBI tools and acronyms, bioinformatics terms and data representation formats.
NCBI Handbook
An extensive collection of articles about NCBI databases and software. Designed for a novice user, each article presents a general overview of the resource and its design, along with tips for searching and using available analysis tools. All articles can be searched online and downloaded in PDF format; the handbook can be accessed through the NCBI Bookshelf.
NCBI Help Manual
Accessed through the NCBI Bookshelf, the Help Manual contains documentation for many NCBI resources, including PubMed, PubMed Central, the Entrez system, Gene, SNP and LinkOut. All chapters can be downloaded in PDF format.

Tools

Amino Acid Explorer
This tool allows users to explore the characteristics of amino acids by comparing their structural and chemical properties, predicting protein sequence changes caused by mutations, viewing common substitutions, and browsing the functions of given residues in conserved domains.
BLAST Tutorials and Guides
This page links to a number of BLAST-related tutorials and guides, including a selection guide for BLAST algorithms, descriptions of BLAST output formats, explanations of the parameters for stand-alone BLAST, directions for setting up stand-alone BLAST on local machines and using the BLAST URL API.
Coffee Break
Part of the NCBI Bookshelf, Coffee Break combines reports on recent biomedical discoveries with use of NCBI tools. Each report incorporates interactive tutorials that show how NCBI bioinformatics tools are used as a part of the research process.
E-Bench
This interactive tool allows users to build E-utility URLs, either from a form or by hand, and then view their raw output. The tool provides a simple environment for testing E-utility URLs before including them in applications.
Ebot
A tool that allows users to construct an E-utility analysis pipeline using an online form, and then generates a Perl script to execute the pipeline.
NCBI Education Page
Provides links to tutorials and training materials, including PowerPoint slides and print handouts.
PubMed Central Tutorials
A series of Flash tutorials on the PubMed Central database, including a general overview as well as discussion of its links to genes, genomes, clinical data, and chemical data in PubChem.
PubMed Tutorials
A collection of web and flash tutorials on PubMed searching and linking, saving searches in MyNCBI, using MeSH and other PubMed services.
Science Primer
A basic introduction to the science and technology that underlies many of the NCBI resources. A great starting place for students and the general public, the Science Primer provides a basis for understanding the NCBI web site and mission, and provides direct links to many NCBI databases and tools. Topics include genome mapping, molecular modeling, mutations, microarrays (gene expression), genetics, pharmacogenomics (personalized medicine) and phylogenetics (evolutionary relationships).

Downloads

FTP: NCBI Field Guide Manual
Downloadable material for NCBI's previously offered Field Guide training course.
FTP: NCBI Structure Course Materials
PowerPoint slides, handouts and exercises for the previously offered NCBI course "Exploring 3D Molecular Structures."