Maximum Interval Window List

Use this option to specify numeric integer values greater than zero, in a space-delimited¹ list, which represent maximum interval windows for each to compute distance between markers on each input linkage map.

One consensus linkage map is generated for each value entered. For example, if the maximum interval window list entered equals to 1 3, two consensus map are estimated.

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For the maximum interval window value of 1 and a linkage map that has markers M1-M2-M3-M4-M5, the distances between M2 and M1, M3 and M2, M4 and M3, M5 and M4, and M5 and M1 (marker interval window of 1) are computed to compose the error term to be minimized. The last distance, between M5 and M1, is part of a wrap-around strategy to keep the length of the consensus map consistent with an average of all input linkage maps2.

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For the maximum interval window value of 3 and a linkage map that has markers M1-M2-M3-M4-M5, the distances between M4 and M1, M5 and M2, M3 and M1, M4 and M2, and M5 and M3 (marker interval window of 3) will be computed to compose the error term to be minimized. The last three distances, between M3 and M1, M4 and M2, and M5 and M3, are part of a wrap-around strategy. Additionally, for this maximum interval window value of 3 there will be distance computed for maximum interval windows 1 and 2, i.e., distances between M3 and M1, M4 and M2, M5 and M3, M4 and M1, and M5 and M2 (marker interval window of 2), and distances between M2 and M1, M3 and M2, M4 and M3, M5 and M4, and M5 and M1 (marker interval window of 1), and the error term to be minimized will be composed of all three marker interval windows.

To Specify Maximum Intervals for Each Linkage Map:

Enter the space-delimited list in the text box, as shown below:

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1

A list is space-delimited when the individual values are separated by a single space.

2

Endelman and Plomion. 2014. Bioinformatics 30(11): 1623–1624