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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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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Literature Cited

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Internet Resources
  NCBI home page.
  NCBI Entrez SNP page.
  NCBI Variation Databases.
  dbSNP build history page.
  Chapter 5 (Kitts, A. and Sherry S. 2009), The Single Nucleotide Polymorphism Database (dbSNP) of Nucleotide Sequence Variation, fromThe NCBI Handbook.
  NCBI Entrez help document.
  dbSNP search help document.
  dbSNP search fields.
  Genetic codes at the NCBI Taxonomy database.
  Genome Reference Consortium.
  dbSNP validation legend.
  Entrez SNP figure legends.
  IUPAC nomenclature code at dbSNP.
  SNP BLAST page.
  Additional dbSNP searching options.
  Genotype query page at dbSNP.
  Gene SNP database.
  International HapMap Project.
  Human Genome Variation Genotype‐to‐Phenotype database, (HGVbaseG2P).
  The Genome Variation Server.
  Pharmacogenomics Knowledge Base (PharmGKB).
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