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10.7554/eLife.07464.005 Figure 3. Parameterisation of the BDP model and inferred details of bottleneck mechanism.
(Based on the resolution of the structure and the quality of electron density maps for residues of Sal and residues of RNAP close to Sal, the inferred proximities of individual residues of Sal to individual residues of RNAP are secure, but the inferred details of H-bonds and van der Waals interactions are, at least in part, provisional).
In a recent comparative study focused on interpolation, which inferred details of patterns of presence and absence on a densely sampled landscape, several techniques that have internal controls on overfitting were superior (34 ).
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From each reconciled gene tree, the orthologous relationships were inferred (for details, see [ Vilella et al. 2009] and http://www.ensembl.org/info/docs/compara/homology_method.html).html
For network inference with the NetGenerator V2.0 tool, several runs were performed with varying configuration parameter values in order to optimize both the 'average MSE' and the number of inferred network edges (for details see Methods section).
Finally, we have demonstrated that our inferred networks can reveal subtle details of genome-scale evolution.
Details of the inferred priming success are provided in Appendix S1, and species-specific notes on primer/sequence mismatches are provided in Appendix S2.
Most surprisingly, we revealed the existence of a Crm1 dimer, whose details could be inferred from crystal contacts observed in an existing Crm1 structure (Dong et al., 2009).
Details for p-value calculations are provided in Additional file 1. 25 connections are shared among the connections in the inferred ODE network and Markov network (details are in Table 1).
These Boolean tables are than translated into links among stimulated, inhibited and measured nodes, giving rise to the inferred network (see Supplementary Material for more details).
A screen of A. niger ATCC 1015 EST sequence data available at the Broad institute (http://www.broadinstitute.org/) demonstrated the presence of an alternative start codon revealing a putative SA with a probability of 0.993 for the newly inferred protein (see Additional File 2 for details).
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