Learn to use the dbSNP resource, a large and valuable NCBI database that serves both as a repository for genomic variation data (including single nucleotide polymorphisms, microsatellites and small insertion/deletion mutations) and as a computational analysis resource. Learning to mine the dbSNP data will provide the researcher with extensive data and information about variations, evolution, disease and more. Understanding the structure of rs identifiers and ss identifiers will provide important conceptual features of SNP stored records within dbSNP and at other sites that employ dbSNP data. Access points from the dbSNP and the EntrezSNP interface will be explored.

You will learn:

  • how to query the database by SNP attributes, submitter and other information
  • how to understand the contents of the rsID records and ssID records
  • where to find detailed information about individual variations
  • how to accomplish additional search types of the database
TUTORIAL RELATED CONTENT

TUTORIALS

This tutorial is a part of the tutorial group Human variations. You might find the other tutorials in the group interesting:

GAD: Genetic Association Database: An archived database associating human genes and polymorphisms with diseases

Madeline 2.0: Human pedigree diagram tools

DrugBank: A chemoinformatics and bioinformatics resource

DGV: Database of Genomic Variants: Database of Genomic Variants, DGV, catalogs and displays structural variation in the human genome

OMIM: Online Mendelian Inheritance in Man (OMIM): A database of human genes, genetic diseases and disorders

CGAP: Characterize the molecular genetic changes that cause a normal cell to become a cancer cell

ENCODE Foundations: ENCyclopedia of DNA Elements

GeneSNPs: An integrated view of gene structure and SNP variations

NIEHS SNPs: National Institute for Environmental Health Sciences Environmental Genome Project (EGP) SNPs

HapMap: HapMap, a database and analysis resource of human variation

Genetics Home Reference: A collection of data describing the effects of genetic variability on human health and disease

dbGaP: A database of genotypes and phenotypes with extensive variation data and clinical details

SeattleSNPs: Human SNPs in genes

GeneTests: GeneTests, a current, comprehensive genetic testing resource

CATEGORIES

Variation & Medical : Resources that include information about sequence variation, phenotypes, or medically-relevant conditions.

NCBI : This category includes resources maintained at the National Center for Biotechnology Information (NCBI).

BLOG POSTS

Friday SNPpets: This week's SNPpets include XKCD for teaching students PSSMs, the 250th eukaryotic genome annotation at NCBI, Galaxy for mobile project checking, missing heritability (not), new dbSNP build, several to...

Video Tip of the Week: PheGenI, Phenotype-Genotype Integrator: The hunt for variations in genes and genomes has been both fruitful and frustrating. We can see genome variations in a variety of ways, but we can't always connect them with a phenotype easily. And vic...

What's the answer? (duplicate dbSNP IDs): BioStar is a site for asking, answering and discussing bioinformatics questions. We are members of the community and find it very useful. Often questions and answers arise at BioStar that are germane t...

Video Tip of the Week: VnD Resource for Genetic Variation and Drug Information: In today's tip I am going to feature a resource that I found recently. I've been updating our dbSNP tutorial, which Mary & Trey will be presenting at workshops in Morocco, and also our free PDB tutori...

What's the answer? (known disease mutations): BioStar is a site for asking, answering and discussing bioinformatics questions. We are members of the community and find it very useful. Often questions and answers arise at BioStar that are germane t...

BIOMED CENTRAL

Recent BioMed Central research articles citing this resource

Wingo S. Thomas et al., MPD: multiplex primer design for next-generation targeted sequencing Results and data. BMC Bioinformatics (2017) doi:10.1186/s12859-016-1453-3

Breusing Corinna et al., Widespread introgression in deep-sea hydrothermal vent mussels Speciation and evolutionary genetics. BMC Evolutionary Biology (2017) doi:10.1186/s12862-016-0862-2

Balikagala Betty et al., Absence of in vivo selection for K13 mutations after artemether–lumefantrine treatment in Uganda. Malaria Journal (2017) doi:10.1186/s12936-016-1663-1

Celik Ibrahim et al., Genome-wide SNP discovery and QTL mapping for fruit quality traits in inbred backcross lines (IBLs) of solanum pimpinellifolium using genotyping by sequencing Plant genomics. BMC Genomics (2017) doi:10.1186/s12864-016-3406-7

Palermo Maria Anna et al., Footprint of the eastern euroasian past in Italian populations of Cryptotaenia thomasii (Ten.) DC Ecology. Botanical Studies (2017) doi:10.1186/s40529-016-0155-5