All simulation sequences were videorecorded and physicians also weared eye-tracking glasses.
In each simulation, sequences were sampled over the course of 2000 generations at a rate of one sample per 2 generations to yield approximately 1000 samples in total.
The simulation sequence is repeated until the target time is reached with the updated values of NAPL saturation, porosity, and effective hydraulic conductivity.
In a simulation of the simplified evolution model, sequences were generated according to a given phylogenetic tree, with parameters including evolution rate and times for each sequence.
Thus, in SCN simulations protein sequences are expected to move around the optimal sequence, so that the evolutionary average of the HP almost coincides with the optimal HP [ 48].
For comparison, two disordered peptides from the sequence-related silk protein (Spidroin-1 and Spidroin-2) and, as a representative of a non-elastomeric protein, two disordered peptides from the vWF linker between domains A1 and A2, were chosen to perform the same collapse force-quench MD simulations (peptide sequences are shown in Additional file 7: Figure S7).
Here the inner EXIT curve is computed through Monte Carlo simulations, when the sequences are taken in blocks of bits, and the power penalty due to the pilot symbols is also compensated for.
When all the sequences are simulated, the simulation will be terminated.
An optimal strategy, which will be a compromise between redundancy suppression and fragment length maximization, can be found by simulation if the cDNA sequences are known.
Authors' response: Part of the supporting data relates to the simulations showing that natural sequences are optimized for overlapping coding with the cox1 region, which is also assumed to code for gau.
