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The ionosphere-to-magnetosphere mapping calculation is also written in IDL and is available from M.F.V. on request ([email protected]).
The results demonstrate clearly that the accuracy of a mapping calculation is very much determined by the schema matcher that is used, and that the system's own matcher, SemMatcher, outperforms the other two matchers in most of the datasets.
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The node setup for a shadow map calculation is shown in Fig. 6.
However, we observed that the genetic map calculation is reasonable because the order of markers on the genetic map is consistent with the order of the physical map positions.
All mapping calculations were carried out in JoinMap V4 [ 62] using the Kosambi function.
The key settings of the texture maps calculation were the radius R of a spherical region of interest around each voxel and the maximum distance d for the texture points.
LOD threshold for map calculation was set as 3.0 except for LG2, LG8 and LG4, in which the LOD scores of 2.0, 2.0 and as low as 0.1 were used respectively, in order to allow the inclusion of more distant loci.
When a marker generated a negative map distance or a large 'jump' value in goodness-of-fit test, the marker was removed, and map calculation was continued to construct a first-round map.
The first step of the recombination map calculation was to determine the best physical order of the markers based on the RH mapping [ 19] and in silico mapping of the SNPs to the pig genome sequence.
When a marker generated a negative map distance in the map or a large "jump" value in goodness-of-fit, which is the normalized difference in chi-square value before and after adding the marker, the marker was removed, and map calculation was continued to construct a first-round map.
All recombination rates up to r = 0.4999 within a linkage group were taken into account to allow the inclusion of more distant loci that are not closely linked, therefore also the LOD threshold for map calculation was set to the minimum of 0.0001.
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