Alignment analysis of these genomic sequences revealed a very high level of similarity (99%) between the sequences at nucleotide level where the majority of mismatches occurred in the intron region (Additional file 4).
Genome-wide divergence (dS, dN, and dN/dS ratio) was calculated between the sequences at early and late time points for the six participants with fibrosis stages available at both serum collections (4 participants with consistent mild disease, 1 participant with conversion from mild to severe disease, 1 participant with consistent severe disease).
This difference was highly significant, also when correcting for small difference between the sequences at pre-test, t(14) = 5.749, p<0.0001.
A position was called a hit if the similarity between the sequence at that position and the Kaiso motif corresponded to at least 90% of the information content present in the motif.
In these adaptation events, the mode of SAMHD1 binding seems to have toggled between recognition sequences at the SAMHD1 N terminus and others located at the C terminus.
Nucleotide diversities represent the average number of nucleotide differences between two sequences at a given site.
The data presented here indicate that Sgs1 acts to suppress recombination between diverged sequences at both the single-end invasion stage and at the strand capture stage.
This method compares the amino acid transition probability scores between 2 sequences at 2 particular sites, using the blocks substitution matrix [ 75].
A typical genetic distance between two sequences at synonymous sites, dS, is ~0.5, although some strains form compact clades and are much closer to each other.
Subfamily classification of GH13, GH30 and GH5 has demonstrated that the majority of the defined subfamilies were monospecific, thus indicating a significantly better correlation of substrate specificity between sequences at the subfamily level than at the family level (Stam et al. 2006; St John et al. 2010; Aspeborg et al. 2012).
