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NCBI Resources: dbVar

Contains information about the NCBI databases to be used as a teaching tool.

dbVar Unique Identifiers

  • nsv - structural variant identifier
  • nstd- study identifier

Boolean Operators

Boolean operators allow you to combine search terms: 

  • AND: Finds documents that contain both terms.
  • OR: Finds documents that contain either term. 
  • NOT: Finds documents that contain the term on the left but not the term on the right.

Advanced Search

By default, Entrez searches your text in "All fields", which looks for the text anywhere in the entry. So if you're getting irrelevant results, try limiting your text to a particular field.

Don't know what fields you can search for? Use the Advanced search

1. Click on advanced beneath the search bar. 

2. Click the drop down menu under Builder to see what fields are stored in gene records.

This is a comprehensive list of all fields you can search for. Fields will vary by database. Example shown here is for the Gene database. 

Need help? Ask Wlad

Searching dbVar

In dbSNP, you can search by

  • Organism: mouse[orgn] returns all reported variations in the mouse 
  • Genedscam[gene] returns all reported variations in the DSCAM gene
  • Chromosome16[CHR] returns all reported variation on mouse chromosome 16
  • Known Variant: nsv1093113: single reference variant with this unique identifier
  • Type of Variant: insertion [Variant Region Type] returns all insertion variants 
  • Study: nstd105 returns all records associated with this study 

These fields can be combined using Boolean Operators to create refined search strategies for dbVar records.

dbVar results page

After submitting your search, a list of results will appear with records that match your query. The results page is divided into 3 columns:

  1. Filters: more ways to limit your search by things like genome location
  2. Results: a list of the Gene records that match your query with basic information
  3. Discovery Column: links to other databases and Search details

You can filter the results by factors like Organism, variant region type (eg: duplication), and the method by which the variation was identified.

The results preview shows the identifier for the variant of interest, type of variant, the study it came from, whether it is clinically relevant, the chromosomal location, and the genes contained in the variant.

dbVar record page

The page for a dbVar record contains information about:

  • Organism
  • Study
  • Type of variant
  • Method to generate data
  • Associated publications
  • Location in the genome

See the following link and image for an example.

http://www.ncbi.nlm.nih.gov/dbvar/variants/nsv1154321/#VariantGenome