Pharmacogenetics of Asthma Treatment
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The following is a brief discussion of the Prettybase format, developed by the SeattleSNPs project for easily representing SNP information for a groups of subjects over a given span of reference sequence. This format is used for input to most of the tools on this website.
The following example shows a prettybase file with 3 loci (000111, 000222, and 000333) in it. The names of these loci correspond to the relative offsets of the SNP locus. Whether these offsets are relative to an absolute chromosome location, a transcription start site, or some reference sequence is irrelevant, as long as they are all within the same coordinate system.
Each locus has been genotyped in 3 (A001, A002, and A003) subjects. Subject names must begin with a single letter which indicates the population to which this subject belongs. Here, "A" indicates that these subjects belong to our "Asthmatic" Population. Some of the tools can use this identifier to split populations and analyze populations seperately. Other than this splitting, this identifier will only effect the labels on certain plots and tables. Other population identifiers include:
The prettybase file described above would look like this:
An example of a prettybase document "in the wild" can bee seen here