Welch Medical Library Guides: Finding Variants Using dbSNP: 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 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 Variation Resources

NCBI maintains a suite of variation resources, including databases, downloadable software and variant data, resources to support the submission of variation data, tools for identifying and visualizing variants, and how-tos related to submitting sequence, determining genotype frequencies, associating variants with diseases, etc.

The following are three core variation databases that are part of this broader collection of resources.

Core Variation Databases from NCBI

ClinVar
A collection of reported relationships, with supporting evidence, between sequence variations and human health.
Database of Genomic Structural Variation (dbVar)
An archive of human large-scale genomic variation, such as large insertions, deletions, translocations, and inversions. In addition to archiving variation discovery, dbVar also stores variant/phenotype associations.
Database of Short Genetic Variations (dbSNP)
An archive of human single nucleotide variations, microsatellites, and small-scale insertions and deletions. dbSNP contains population-specific frequency data, molecular context, and mapping information for both neutral variations and clinical mutations.