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Genome Scanner Help

Tool Description

The purpose of Genome Scanner tool is to facilitate selecting polymorphic markers by utilizing several datasets: the Allele Characterization Project dataset in combination with various genetic and Radiation Hybrid maps. Its primary purpose is to support genetic mapping projects where the selection of polymorphic markers between two strains is a major task. SSLPs are the marker of choice for these experiments as they exhibit a wide variety of inter-strain variability.

Finding polymorphic markers using Genome Scanner

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:

  1. Select the two strains to be crossed
  2. 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)
  3. Select the chromosome(s) to be analyzed
  4. Leave the remaining options unaltered
  5. 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.

Bin Size:

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

Output options

Highlight allele size differences between:

Choose a size range in base pairs.

Output Content:

Choose the output combination of chromosome statistics and polymorphic markers with the drop-down menu.

Output Format:

Choose the output to be in HTML or CSV format by using the drop-down menu.


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The Genome Scanner Results

Based on the selected Genetic or RH map, markers that are polymorphic between the two selected strains are organized into bins based on the desired scan resolution. For example, to pick polymorphic markers for a 10cM genome scan you would select a 10cM bin size and you could then pick one marker from each 10cM bin and thereby get coverage of the desired chromosome(s) at the desired resolution.

Sample results are shown below for a cross between FHH and ACI using the Radiation Hybrid map and a bin size of 50cR for an analysis of chromosome 20.

 Chromosome report
This table shows the length (in cR for this example), the number of 50cR bins along the chromosome, the proportion of polymorphic markers and the polymorphism percentage (23/39 x 100)

 Below the report is the Polymorphism table:
This shows the first two bins on Chromosome 20. The first three columns are related to the map (the marker, its position, the LOD score of its placement), followed by the marker allele size in the two strains and the difference between the two sizes. If the difference is in the range selected on the original form (4-20bp in this example) it is highlighted in green. The checkbox allows the selection of one or more markers from each bin to assemble into a run list for a genome scan.

  At the end of the polymorphism table, a second form allowing the user to assemble all the selected markers (add to runlist option checked) into a single runlist for use in the lab.
 Clicking ‘Generate Runlist’ will return a new page (or text file depending on the output format) listing just the selected markers:
 This can then be printed out or saved and provides a list of the polymorphic markers to be used in a genome scan experiment, along with the expected sizes in each strain.

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Related Information/Links

Information related to polymorphic markers can also be found in the strain reports for various inbred strains. This can be very useful when selecting strains to use in a genetic mapping cross as one can view the strain’s description and also see if there are SSLP markers genotyped in that strain.

The SSLP reports list the allele size data available for that SSLP in each of the strains for which data is available.


RGD is funded by grant HL64541 from the National Heart, Lung, and Blood Institute on behalf of the NIH.