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Genome Scanner Help
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| RGD Definition | ||||
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"This tool is to assist researchers in selecting polymorphic markers for a genome scan of a cross between two strains. It uses the Allele Characterization Project dataset in combination with various genetic and Radiation Hybrid maps (also see RH Map Server)." 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. [ back to top ] |
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| 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:
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.
Below is a more detailed explanation of each element of the Genome Scanner form. Genome Scanner form help here! Choose... Enter a ... to search for... Enter the Bin Size.... 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 Highlight allele size differences between. Put the ...... Put the ...... [ back to top ] |
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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. [ back to top ] |
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| The Genome Scanner Results | ||||
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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. 1. 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 * 100%) Below the report is the Polymorphism table itself: 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. [ back to top ] |
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© Bioinformatics Program, HMGC at the Medical College of Wisconsin
RGD is funded by grant HL64541 from the National Heart, Lung, and Blood Institute on behalf of the NIH.