We have developed a genotype classifier for identifying unknown simple sequence repeat (SSR) genotypes of Phytophthora infestans. Users can upload 12-plex SSR profiles of unknown isolates and query them against a global database of known genotypes to find the closest match to their sample.
General guide to usage
After extracting DNA from a sample of P. infestans, use the 12-plex SSR system developed by Li et al. 2013 to genotype the sample. This system uses a set of 12 primers and 4 fluorescent dyes to generate an allelic profile that can then be used to compare the sample against the SSR classifier’s database. Methods for both genotyping the samples and processing the resulting data are described in the link below.
In order to use the SSR classifier, allelic profiles should be formatted as a csv file. This sample file can be downloaded and used as a template for your data. Multiple samples can be included in the same file to allow for batch uploads into the classifier.
Once your data have been formatted, you can upload the csv file to the classifier, which will then use Bruvo’s distance to compare your data to the genotype database and find the closest matches.