As expected, the alignment accuracy in CpG island simulation data is substantially improved by suppressing multiple alignments (Table 10A, B).
To test the fidelity of this approach, we applied it to each of the twelve reference strains and compared its results to the accessory genome sequences previously generated by multiple alignments (Table 1).
Multiple sequence alignment (Table 2, Figure S1 and Table S2) indicates that G263 and V267 of ATEG_03630 occupied the same positions as N235 and S240 of DhbE, respectively.
For each of the predicted antigenic peptides, the average variability index was calculated mutation types were identified and all possible combinations of mutations were identified from multiple sequence alignment (Table 3).
A single nucleotide difference between L. caesar and L. illustris (position 42 in intron 2, multiple alignments in Table 2) could distinguish the two closely related species; cytosine (C) is present in this location in L. caesar and adenine (A) in L. illustris.
Each type of interactive content has its own functionality: 3D molecules (Fig. 4), for example, can be rotated, zoomed and rendered in a variety of styles (e.g. space-fill, backbone or cartoon); sequences and their associated features can be inspected individually, or edited as multiple alignments; and tables of data can be manipulated or converted automatically into scatter-plots or histograms.
These HC amino acids are indicated with asterisks in the multiple alignment and in the supplemental tables (Tables S1-S3, see Additional File 1).
For the means in Table 2, multiple alignment was selected directly and the results automatically recorded.
Protein sequences of BVMOs (Additional file 1: Table S1) were aligned with MAFFT (Multiple Alignment using Fast Fourier Transform) version 7 (Katoh and Standley 2013).
Strategy 1 uses only multiple alignment across all four species (see Table 2 for the sequence space).
