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b) dbSNP compiles identical ss# records into one reference SNP cluster (rs#) containing data from each ss#. c) Users can retrieve data for specific rs# records and analyze these variations. d) Data from dbSNP aids clinical and applied research. The ss# and rs# IDs in this figure are examples only.
Single nucleotide polymorphism annotation (SNP annotation) is the process of predicting the effect or function of an individual SNP using SNP annotation tools. In SNP annotation the biological information is extracted, collected and displayed in a clear form amenable to query.
The SNP file format was used by Microsoft Access to store Report Snapshots in a single file which can be viewed and printed by the Microsoft Snapshot Viewer, a Windows program available free of charge from Microsoft that allows report output to be viewed without requiring Access. Support for the format was discontinued in Access 2010 and later ...
A SNP array can also be used to generate a virtual karyotype using software to determine the copy number of each SNP on the array and then align the SNPs in chromosomal order. [10] SNPs can also be used to study genetic abnormalities in cancer. For example, SNP arrays can be used to study loss of heterozygosity (LOH). LOH occurs when one allele ...
An example of cluster sampling is area sampling or geographical cluster sampling.Each cluster is a geographical area in an area sampling frame.Because a geographically dispersed population can be expensive to survey, greater economy than simple random sampling can be achieved by grouping several respondents within a local area into a cluster.
Converts various file formats to the custom ANNOVAR input file format. See "Conversion to the ANNOVAR input file format" section. .avinput table_annovar.pl: automated variant annotator A wrapper around annotate_variation.pl that can take VCF format along with the ANNOVAR format, performs annotation and outputs an Excel-compatible file. Ideal ...
1. Introduce the reference of a SNP of interest, as an example: rs429358, in a database (dbSNP or other). 2. Find MAF/MinorAlleleCount link. MAF/MinorAlleleCount: C=0.1506/754 (1000 Genomes, where number of genomes sampled = N = 2504); [4] where C is the minor allele for that particular locus; 0.1506 is the frequency of the C allele (MAF), i.e. 15% within the 1000 Genomes database; and 754 is ...
In the oligonucleotide ligase assay, two probes are designed; an allele-specific probe which hybridizes to the target DNA so that its 3' base is situated directly over the SNP nucleotide and a second probe that hybridizes the template upstream (downstream in the complementary strand) of the SNP polymorphic site providing a 5' end for the ...