In this work, we explore simulations of a more realistic sequence-based model of transcription factor DNA binding, which overcomes limitations of the theoretical model.
In more realistic terms, sequence stratigraphy establishes the analysis of cyclic sedimentation patterns that are present in stratigraphic successions as they develop in response to various variations in sediment supply and accommodation (Posamentier and Allen 1999).
Simulations with our new Purkinje network predicted more realistic activation sequences and activation times than simulations without.
However, the nature of local alignment can be markedly different when we adopt more realistic and complex sequence alignment models that capture evolutionary constraints at a higher level than primary sequence alone.
Likewise, analyses under more realistic models of sequence evolution, taking into account differences in evolution between stem and loop regions of rRNA, did not differ markedly from analyses using standard four-state models.
The other is to employ more realistic models of sequence evolution that account for various systematic biases [ 13, 15, 45].
Much discussion was devoted to the need for more realistic models of sequence evolution, which would enable the proper assessment of what level of similarity is expected for two evolutionary related sequences.
For example, phylogenetic analysis indicated an LGT origin of the T. vaginalis hydrogenosomal NuoF protein distinct from the mitochondrial homologs [ 86], a conclusion shown likely to be incorrect upon re-analysis using more realistic models of sequence evolution [ 87].
Nevertheless, this model clearly oversimplifies the complex evolutionary processes involved, and in the future, it would be interesting to investigate the effect of a more realistic model of sequence evolution on AED detection, once sequencing/annotation errors have been removed.
Although the use of relaxed clocks and more realistic models of sequence evolution can mitigate the problem of rate heterogeneity, the lack of robust calibration points remains a major challenge to established a timescale for bacterial evolution.
We assume that phylogenetic analyses based on these genes can be improved further i) by enlarging the taxon sample and ii) employing more realistic models of sequence evolution incorporating non-stationary substitution processes and iii) considering covariation and pairing of sites in rRNA-genes.
