Single nucleotide polymorphisms (SNPs) are sites of single base-pair variations found in populations. As possible markers for loci of phenotypic traits, there is considerable interest in finding the locations of these sites. Using array comparative genomic hybridization (aCGH), we have created a method to detect novel SNPs using overlapping probes targeting a finite range.
The SNP selection application selects the individual oligo sequences to be used in the aCGH process to detect SNPs. Currently, the application is available for the WS190 C. elegans and R5.12 D. melanogaster genomes. Additional fasta files can be uploaded and processed but the functionality will be limited as it is impossible to filter out repeats or select for exons.
The application is available here:
http://hokkaido.bcgsc.ca/SNPdetection/cgi-bin/probeselection.cgi
Once an experiment is completed using the supplied oligos, log2 ratios of the sample and reference can be used to look for possible anomalies. These are sites of possible polymorphisms. The ratio calculator program allows users to upload their sample and reference .pair files in order to calculate the normalized log2ratio values. Additionally, the oligo file supplied by the experiment can also be uploaded to further add to the annotations in the output.
The log2 ratio application is available here:
http://hokkaido.bcgsc.ca/SNPdetection/cgi-bin/ratiocalculator.cgi