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NCBI's SNP database

Tutorial and training materials by OpenHelix

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.
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You'll 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


Categories

View additional tutorials for resources in

  • Variation & Medical
  • NCBI : This category includes all resources maintained at the National Center for Biotechnology Information (NCBI)

Recent BioMed Central research articles citing this resource

Matsunami Nori et al., Identification of rare DNA sequence variants in high-risk autism families and their prevalence in a large case/control population. Molecular Autism (2014) doi:10.1186/2040-2392-5-5

Hosang M Georgina et al., Interaction between stress and the BDNF Val66Met polymorphism in depression: a systematic review and meta-analysis. BMC Medicine (2014) doi:10.1186/1741-7015-12-7

Holmquist Peter et al., Urine π-Glutathion S-transferase but not Tamm-Horsfall protein correlates with Carotid artery intima media thickness in childhood type1 diabetes Hypertension and Cardiovascular Risk. BMC Cardiovascular Disorders (2014) doi:10.1186/1471-2261-14-39

Tayubi Aslam Iftikhar et al., In silico analysis of detrimental mutation in EPHB2 gene causing Alzheimer’s disease Abstracts from the 2nd International Genomic Medicine Conference (IGMC 2013) 2nd International Genomic Medicine Conference (IGMC 2013). BMC Genomics (2014) doi:10.1186/1471-2164-15-S2-P46

Pár Alajos et al., IL28B and IL10R −1087 polymorphisms are protective for chronic genotype 1 HCV infection and predictors of response to interferon-based therapy in an East-Central European cohort. BMC Research Notes (2014) doi:10.1186/1756-0500-7-12

More about the resource:

dbSNP is one of the many useful resources supported by the National Center for Biotechnology Information, or NCBI, and acts as a repository for individual submissions from labs and institutions, and provides interfaces to search, retrieve, and display a wealth of information about variation in many species. Additionally, reference variation data is computed from the entire database of individual variation submissions. dbSNP can be browsed or queried in several ways, including basic searches on submission type, SNP attributes, submitter information and much more. Additionally, there is advanced searching using the Entrez system.


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The materials and slides offered can not be resold or used for profit purposes. Reproduction, distribution and/or use is strictly limited to instructional purposes only and can not be used for for monetary gain or wide distribution.
Copyright 2009, OpenHelix, LLC.

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