Welch Medical Library Guides: Finding Sequence Using NCBI Nucleotide: The National Center for Biotechnology Information (NCBI)

NCBI's Scope

The National Center for Biotechnology Information (NCBI) is part of the National Library of Medicine at the National Institutes of Health. NCBI supports research in computational biology, develops software tools for sequencing analysis, and creates and maintains public bioinformatics databases.

It provides BLAST, a tool for determining sequence similarity. And among its many databases for exploring human and other genomes are Nucleotide for sequence, dbSNP for small-scale variation, and Gene for comprehensive, aggregated information relating to individual genes.

NCBI as a Genomics Gateway

The phrase "genomics gateway" is used here to refer to an online collection of databases and tools related to genomes and genes.

Genomics gateways have a broad scope, typically encompassing databases on genes, variation, sequence, gene expression, genotype-phenotype relationships, etc. Examples of genomics gateways include those maintained by the NCBI, EMBL-EBI and SRI International (e.g., BioCyc).

Additional features of genomics gateways include:

Maintenance by stable, governmental and/or non-profit parent organizations (e.g., the National Center for Biotechnology Information)
Participation in international consortia for genomics information sharing (e.g., the International Nucleotide Sequence Database Collaboration)
Extensive linkages between databases within gateways (e.g., between the Ensembl Genome Browser and the Expression Atlas)
Extensive linkages between databases across gateways (e.g., between NCBI Gene and BioCyc)

Genomics gateways are excellent destinations for launching explorations of genes and genomes. They offer similar searching and analysis tools and work from a shared set of genomic data. Despite this similarity, each repository has unique functionalities for discovery, visualization, and analysis.

NCBI's DNA and RNA Resources

NCBI maintains a suite of DNA and RNA resources, including databases, downloadable software and sequence collections, resources to support the submission of sequence and other data, tools for searching and sequence analysis, and how-tos related to submitting sequence, finding sequence, designing PCR primers, etc.

The following are four core genomic sequence databases that are part of this broader collection of DNA and RNA resources.

Core Genomic Sequence Databases from NCBI

GenBank
An annotated collection of all publicly available DNA sequences. Part of the International Nucleotide Sequence Database Collaboration. It includes sequences generated using Sanger sequencing and assembled sequences generated using next generation sequencing technologies.
Nucleotide
Organizes and makes searchable sequence data from multiple sources, including NCBI's GenBank and RefSeq databases
Reference Sequence Database (RefSeq)
Contains curated, non-redundant sequences for genomic DNA, transcript (RNA), and protein, providing stable reference points for further study.
Sequence Read Archive (SRA)
Stores raw sequencing data and alignment information from next generation sequencing projects.

Note: Nucleotide provides powerful tools for building complex searches of GenBank and RefSeq sequences. See the "Searching the Nucleotide Database" and "A Search Example in Five Steps" sections of this guide for a description of these tools as they are applied to particular use cases.