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After the mutational mapping, we performed in silico mutagenesis to observe the effects of the mutations on the interactions.
Difference Mapping We performed 2D difference mapping between class averages by first aligning, rotating, and shifting them in IMAGIC (van Heel et al., 1996 ) using the MSA-ALIGN command.
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What sets our approach apart from existing methods is the "global" use of SR mapping: we perform an SR mapping step for all orphaned or substantially soft-clipped reads before the detection begins, and therefore both RP and SR mappings are available at the outset, and can nucleate SV event calls.
Briefly, on each map, we performed Principal Component Analysis, and the first component was taken.
To construct the linkage map, we performed re-sequencing of the parents and designed BeadArray markers using detected single nucleotide polymorphisms (SNPs).
To test the temporal stability (i.e., repeatability) of S-maps, we performed the following three-step analysis.
Then, for each noisy contact map we performed 10 different reconstructions.
With eigenvector centrality maps we performed paired t tests between the placebo and exenatide conditions for each scanning block.
In order to interpret the maps, we performed flexible fitting of suilysin domains from the crystal structure.
Visualization of and Docking into 3D Maps We performed 3D structure analysis and image rendering using the UCSF Chimera package (Pettersen et al., 2004 ).
Using phenotypic values, as mentioned above, and our linkage map, we performed a QTL analysis for GA-responsive TIL, LEI and NEI (qGTIL, qGLEI and qGNEI).
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