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. | Advertisement:
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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
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| Recent BioMed Central research articles citing this resourceVenturini Luca et al., De novo transcriptome characterization of Vitis vinifera cv. Corvina unveils varietal diversity Plant genomics. BMC Genomics (2013) doi:10.1186/1471-2164-14-41 Chen Quan et al., A unified approach for allele frequency estimation, SNP detection and association studies based on pooled sequencing data using EM algorithms Selected articles from the Eleventh Asia Pacific Bioinformatics Conference (APBC 2013): Genomics The Eleventh Asia Pacific Bioinformatics Conference (APBC 2013). BMC Genomics (2013) doi:10.1186/1471-2164-14-S1-S1 Ragheb N Mark et al., The mutation rate of mycobacterial repetitive unit loci in strains of M. tuberculosis from cynomolgus macaque infection Prokaryote microbial genomics. BMC Genomics (2013) doi:10.1186/1471-2164-14-145 Trushina Naomi et al., PacC and pH–dependent transcriptome of the mycotrophic fungus Trichoderma virens Eukaryote microbial genomics. BMC Genomics (2013) doi:10.1186/1471-2164-14-138 Porcellini Elisa et al., Monocyte chemoattractant protein-1 promoter polymorphism and plasma levels in alzheimer’s disease. Immunity Ageing (2013) doi:10.1186/1742-4933-10-6 |
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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