Searching NCBI's dbSNP Database

Medha Bhagwat1

1 NIH Library, Office of Research Services, National Institutes of Health, Bethesda, Maryland
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 1.19
DOI:  10.1002/0471250953.bi0119s32
Online Posting Date:  December, 2010
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Abstract

The Single‐Nucleotide Polymorphism database (dbSNP) is a variation database at the National Center for Biotechnology Information (NCBI). It is a public repository of submitted nucleotide variations and is part of NCBI's search and retrieval system Entrez. This unit describes two basic protocols to search dbSNP effectively, one to perform a text‐based search and another to perform a sequence‐based search. The unit also describes one of the result display formats called GeneView to obtain information about all submitted SNPs in a particular gene. Curr. Protoc. Bioinform. 32:1.19.1‐1.19.18. © 2010 by John Wiley & Sons, Inc.

Keywords: single‐nucleotide polymorphism (SNP); variation; NCBI; dbSNP

     
 
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Table of Contents

  • Introduction
  • Basic Protocol 1: Searching dbSNP Using the Entrez Limits Search Option
  • Alternate Protocol 1: Searching dbSNP Using the Entrez Preview/Index Search Option
  • Basic Protocol 2: Searching dbSNP Using a Query Sequence
  • Commentary
  • Literature Cited
  • Figures
     
 
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Materials

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Figures

Videos

Literature Cited

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Internet Resources
   http://www.ncbi.nlm.nih.gov/
  NCBI home page.
  http://www.ncbi.nlm.nih.gov/sites/entrez?db=snp
  NCBI Entrez SNP page.
  http://www.ncbi.nlm.nih.gov/guide/variation/
  NCBI Variation Databases.
   http://www.ncbi.nlm.nih.gov/projects/SNP/buildhistory.cgi
  dbSNP build history page.
   http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=handbook&part=ch5
  Chapter 5 (Kitts, A. and Sherry S. 2009), The Single Nucleotide Polymorphism Database (dbSNP) of Nucleotide Sequence Variation, fromThe NCBI Handbook.
   http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=helpentrez&part=EntrezHelp
  NCBI Entrez help document.
  http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=helpsnpfaq&part=Search
  dbSNP search help document.
  http://www.ncbi.nlm.nih.gov/snp
  dbSNP search fields.
  http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=tgencodes
  Genetic codes at the NCBI Taxonomy database.
  http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/index.shtml
  Genome Reference Consortium.
  http://www.ncbi.nlm.nih.gov/projects/SNP/snp_legend.cgi?legend=validation
  dbSNP validation legend.
  http://www.ncbi.nlm.nih.gov/corehtml/query/Snp/EntrezSNPlegend.html
  Entrez SNP figure legends.
  http://www.ncbi.nlm.nih.gov/SNP/iupac.html
  IUPAC nomenclature code at dbSNP.
  http://www.ncbi.nlm.nih.gov/projects/SNP/snp_blastByOrg.cgi
  SNP BLAST page.
  http://www.ncbi.nlm.nih.gov/projects/SNP/
  Additional dbSNP searching options.
  http://www.ncbi.nlm.nih.gov/projects/SNP/snp_gf.cgi
  Genotype query page at dbSNP.
  http://www.genome.utah.edu/genesnps/
  Gene SNP database.
  http://hapmap.ncbi.nlm.nih.gov/
  International HapMap Project.
  http://www.hgvbaseg2p.org
  Human Genome Variation Genotype‐to‐Phenotype database, (HGVbaseG2P).
  http://gvs.gs.washington.edu/GVS/
  The Genome Variation Server.
  http://www.pharmgkb.org/
  Pharmacogenomics Knowledge Base (PharmGKB).
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