Finding Variants Using dbSNP

This guide is based on a Welch Medical Library class on finding gene-based information using the web interface of the National Center for Biotechnology Information (NCBI).

This guide:

• Situates the Database of Short Genetic Variations (dbSNP) in the broader context of NCBI's mission and NCBI's suite of related databases
• Summarizes dbSNP's content, scope, and searching features
• Walks users step-by-step through a use case on finding functionally-significant variants for genes in a particular biological pathway

Far from an exhaustive look at dbSNP, this guide nevertheless provides an excellent starting point for understanding its scope and effectively searching its content.

After reading through this guide, users will be able to do the following in the dbSNP database:

• Use a concept-based approach to searching

• Use trusted sources for finding pathway genes, gene names, and biological sequence features when constructing searches

• Use advanced searching tools, such as fields tags, Boolean operators, and index lists

• Navigate and export search results

A hands-on companion class from the Welch Medical Library called "NCBI Nucleotide, Gene, and dbSNP Databases" exists for this guide. It is currently offered a few times a year. Check the Welch Classes calendar for the next offering of the class.

Class Description

The Nucleotide, Gene, and dbSNP databases from the National Center for Biotechnology Information (NCBI) provide a wealth of gene-based information. Nucleotide organizes and makes searchable sequence data from multiple sources, including GenBank and RefSeq. Gene provides detailed information, including gene ontology and genomic context, for known and predicted genes from all major taxonomic groups. And dbSNP archives human single nucleotide variations, microsatellites, and small-scale insertions and deletions.

This class outlines the content, scope, and searching features of NCBI’s Nucleotide, Gene, and dbSNP databases. Real-world searching scenarios are presented for finding sequence, gene ontology, and variants. Participants are guided live through hands-on searching workflows using the web interfaces of each database. Participants learn how to:

• Use a concept-based approach to searching
• Use trusted sources for finding gene names and gene ontology when constructing searches
• Use advanced searching tools, such as fields, truncation, quotation marks, Boolean operators, and index lists
• Navigate and export search results

Additional Related Guides

Two additional guides have been developed based on this class: "Finding Sequence Using NCBI Nucleotide" and "Finding Gene Attributes Using NCBI Gene". These guides are structured just like the guide you are using now and present similar information, including:

• The context of Nucleotide and Gene databases in NCBI's mission and suite of related databases
• The content, scope, and searching features of Nucleotide and Gene
• Use cases on how to retrieve specific kinds of biological data from these databases