A general problem in evolutionary biology is how to reconstruct the phylogenetic tree from sequence data obtained from sampled individuals.
Data analysis techniques have been developed in the past decade that extract the maximum structural detail from reflectivity data obtained from samples with complex deuteration schemes while avoiding overinterpretation.
Whereas electron microscopy and scattering data point somewhat more to a hairpin model of β-fibrils, ssNMR data obtained from samples with selectively labelled peptides are in agreement with both, hairpin structures and linear arrangements.
Results: Applying ViVan on deep sequenced data obtained from samples that were previously characterized by more classical approaches, we uncovered novel and potentially crucial aspects of virus populations.
Instead of deriving k from the ratio of signals in heterozygous individuals, we suggest deriving it from pooling data obtained from samples of reference individuals from whom DNA and vast quantities of genome-wide genotype data are available through cell repositories and the HapMap respectively.
In this situation, a topological study of fibril structure by hydroxyl radical footprinting (HRF) and mass spectrometry is useful to test these models and to determine if structural constraints obtained for fibril samples in water are compatible with models that rely on data obtained from samples prepared for SS-NMR.
Applying ViVan on deep sequenced data obtained from samples that were previously characterized by more classical approaches, we achieved superior sensitivity and uncovered novel and potentially crucial aspects of virus populations, which could not have been identified otherwise and in much shorter time scales.
Sequencing data obtained from samples A and P were pooled and subjected to a publicly available sequence cleaning and validation software, SeqClean [ 71], to account for size-selection, overall low complexity analysis, and to remove poly (A T) regions, and adapters.
Bisulfite sequence data were obtained from sampling six or seven glands each from opposite tumor halves (see Figure 2).
DEM results were validated using experimental data obtained from both sampling and image techniques.
