Explanation of input
In order to save search time, we need you to give a set of markers all
from the same chromosome and provide us with the number for that chromosome (enter 23
or X for the X chromosome).
We form a framework map using the input markers, where adjacent markers
on this map are separated by at least one (or two) observed recombination events. By
choosing 1, a longer framework map will be produced, but there will be a greater
chance that some of the markers are not in the correct order. By choosing 2, fewer
markers are placed on the framework map, but the markers are ordered with greater
reliability.
When forming the framework map, we may either weight the markers
according to their heterozygosity, using weights of the form -log(1-het), and finding the
framework map where the sum of the weights is maximized, or, alternatively, we may give
equal weight to all markers, and then find the framework map with the largest number of
markers. Choose Yes to weight the markers according to their heterozygosity, or No
to weight the markers equally.
Note: The form of the weights, w(het) = -log(1-het), was
derived assuming that the markers are in Hardy-Weinberk equilibirum and linkage
equilibrium. In this case, consider three markers with heterozygosity het1, het2 and het3,
where w(het1) + w(het2) = w(het3). Then the chance that an individual is heterozygous for
at least one of the first two markers is equal to the chance that he or she is
heterozygous for the third marker.
Enter the markers either as probe names (such as AFMa127zc9) or locus
name (such as D1S2644). The search is not case-sensitive. The markers should all be on the
same chromosome.
The output will contain a list of markers which were not found, as
well as a list of markers which have been identified as “cryptic duplicates,”
corresponding to the same locus as another marker on the map, but with different PCR
primers.