In addition, there are no strong correlations between structure size (the average length of pairwise alignment within a family) and bilinear correlation (r = 0.42, p<0.01).
The similarity of a sequence alignment is determined by the average pairwise sequence identity (APSI) of that alignment.
If the average pairwise similarity in the multiple alignment of one domain was below 70percentt and/or more than 5 positions in the consensus sequence correspond to an 'X', we validated the alignment and consensus sequence manually.
Our bias-free subtomogram processing uses unsupervised hierarchical ascendant classification and averaging (HAC), a technique involving pairwise alignment of sub-tomograms and clustering based on similarity (Bartesaghi et al., 2008; Förster et al., 2008; Schmid and Booth, 2008), without the aid of a reference and without imposing symmetry at any point.
Consensus sequences were aligned across all taxa, yielding a 319 bp alignment with an average pairwise sequence similarity of 99.8%, with 317 sites (99.4%) identical across all taxa, no stop codons and no indels.
Consensus sequences for each of the putative PHYC contigs were aligned across all taxa, yielding a 1,022 bp alignment with an average pairwise sequence similarity of 99.1%, 1,002 sites (98.0%) identical across all taxa, with no indels or stop codons in any taxa.
Results from mothur (with preclustering, pairwise alignment and the average linkage) are also shown in Figure 6 for comparison.
Based on these pairwise alignment scores, an average genomic distance matrix has been computed (Table 5) and a phylogenetic tree constructed.
The average pairwise sequence identity (APSI) of the alignment is 84.8%; the four EBV strains were close in sequence (APSI of 95.6%), while MHV4 had an APSI of 68.6% versus EBV.
PHYE hinge region consensus contigs from our study taxa formed a 270 bp alignment with an average pairwise similarity of 98.9%, with 264 (97.8%) invariant sites, no indels, and no stop codons in any taxa.
