GenomeScanner allows you to select polymorphic markers between two strains either for the entire genome (for a whole genome scan for example) or for one or more chromosomes (for high density mapping studies).
The basic steps to use GenomeScanner are:
- Select the two strains to be crossed
- Select a map upon which to base the analysis (allows markers to be ordered across the genome, the RH 2.2 map is the most dense map and is the recommended map selection)
- Select the chromosome(s) to be analyzed
- Leave the remaining options unaltered
- Click the Submit button
The tool will return a list of the SSLP markers that are polymorphic between the two strains for the chromosome(s) selected. The allele sizes in the two strains are listed along with the size difference between the two sizes. The results are described in greater detail below.
Try Genome Scanner
Below is a more detailed explanation of each element of the Genome Scanner form.
Select Cross, map, desired bin size and chromosome
Choose strains from drop-down menus.
Available Maps at RGD:
Choose a map from the drop-down menu.
Enter the Bin Size (10-200) from the the drop-down menu. The units are cM for Genetic maps and cR for RH maps.
Restrict the returned genes to ones mapped to a particular chromosome. Excludes genes that are unmapped or mapped to a different chromosome
Highlight allele size differences between:
Choose a size range in base pairs.
Choose the output combination of chromosome statistics and polymorphic markers with the drop-down menu.
Choose the output to be in HTML or CSV format by using the drop-down menu.
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