A typical analysis interval was 3 min per sample after optical alignment and background measurement.
Because the differential image imposes built-in contrast resulting from imperfection in the gratings and their alignment, a background differential phase image was measured without a sample in the field of view prior to the tomographic scan.
For each value of n, we compared the distribution of scores for the (i, i + n) pairs to the distribution of all other positions pairs in the alignment (the background distribution) using a one-tailed (H a : μ other < μ n ), two-sample t-test.
We compared two sets of models, the first set focused on comparing changes in ω (= dN/ dS) along the branches of the tree, and the second set of models focused on comparing changes in ω along the different sites in the alignment between background and foreground sets of branches.
Prior to selection analysis, we screened both partial haemocyanin regions for conserved and variable sites using the Jensen-Shannon Divergence [ 30], which identifies conserved sites as deviations of a probability distribution from the overall amino acid distribution of the respective BLOSUM62 alignment as background and also accounts for conservation in neighbouring sites.
A further possible detection of the brown dwarf candidate Roque 9, with log LX ≈ 27.8 and X-ray-to-bolometric luminosity ratio of log(LXLbol) ≈ −2.5, may be due to a chance alignment with a background source.
The algorithm uses a sliding window method to determine if a query sequence from an individual matches sequences in a background alignment of viral sequences derived from that individual and his partner.
Among these residues, Q791 in the inter-lobe linker contributes the most (indicated by the height of the histogram in Figure 1) to ErbB functional divergence, since none of the RTKs outside of the ErbB family conserve a glutamine at the 791 position (Background alignment in Figure 1).
This later step often involves further data alignment such as background adjustment or data aggregation such as per-biomarker summarization from multiple subset measurements.
