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OpenHelix

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

Killeen P Aideen et al., Global gene expression in endometrium of high and low fertility heifers during the mid-luteal phase of the estrous cycle Non-human and non-rodent vertebrate genomics. BMC Genomics (2014) doi:10.1186/1471-2164-15-234

Wang Ningning et al., Mutation of the RDR1 gene caused genome-wide changes in gene expression, regional variation in small RNA clusters and localized alteration in DNA methylation in rice Genomics and evolution. BMC Plant Biology (2014) doi:10.1186/1471-2229-14-177

Black A Holly et al., Inferring mechanisms of copy number change from haplotype structures at the human DEFA1A3 locus Human and rodent genomics. BMC Genomics (2014) doi:10.1186/1471-2164-15-614

Vundinti Babu Rao et al., Chromosomal instability and molecular mutations in multi spectrum disease of Fanconi anemia Proceedings of the International Conference on Human Genetics and 39th Annual Meeting of Indian Society of Human Genetics International Conference on Human Genetics and 39th Annual Meeting of the Indian Society of Human Genetics (ISHG). Molecular Cytogenetics (2014) doi:10.1186/1755-8166-7-S1-I47

Saatchi Mahdi et al., Large-effect pleiotropic or closely linked QTL segregate within and across ten US cattle breeds Non-human and non-rodent vertebrate genomics. BMC Genomics (2014) doi:10.1186/1471-2164-15-442

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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