3′ UTRs were folded locally using RNAplfold (Bernhart et al., 2006), allowing the maximal span of a base pair to be 40 nucleotides, and averaging pair probabilities over an 80 nt window (parameters -L 40 -W 80), parameters found to be optimal when evaluating siRNA efficacy (Tafer et al., 2008).
In order to compare the SOLiD and Genome Analyzer platforms under optimal conditions for each platform and to compare in a manner the majority of end-users are likely to employ, the manufacturers used parameters determined to be optimal for SNP calling on their particular platform.
Thus, the analysis was repeated only using the Enterobacteriaceae dataset for the training, and the same parameters that were found to be optimal in cross-validation.
These vibration parameters have been found to be optimal for the induction of human osteoblast-like cells proliferation and metabolic activity.
For all algorithms, we adjusted parameters to obtain what appeared to be optimal results on the tested dataset.
It is however important to note that for an accurate comparison of predictive power, the inferred parameters of the kinetic model have to be optimal.
If, then reaches the minimum when, so is said to be optimal control parameter of process (2.1).
All optimal designs given in the previous sections assume prior knowledge about the parameters to be expected and are optimal only when these parameters are indeed the true parameters (so-called locally optimal designs, Chernoff 1953).
We ran BWA with default parameters as well as with adjusted parameters (e.g., changing number of permitted gaps and maximum edit distance) but found the default parameters to be the most optimal with our dataset in terms of mapped reads.
More data is still desirable to better define the exact parameters to be followed and their optimal thresholds, and to delineate the optimal cost-effective interventions for these patients.
