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We have described a novel approach using base composition analysis for viral identification.
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Thus, for use in human clinical diagnostics, base composition analysis of the 2 target regions described here would provide corroborative information and accurate species identification of CoV infections.
In this study, sequence variation of mGing was firstly observed by base composition analysis of its TIR region.
Base composition analysis of TIRs indicated that two TIR sequences were not perfectly conserved among mGing copies.
To determine the utility of base composition analysis in the search for animal CoV species, we calculated the cumulative mutation distances for both target regions for all known CoV and plotted groups where all members fall within certain probability thresholds, as shown in Figure 4.
Even though the base composition analysis is not as informative as sequencing, it has enough discrimination power for the detection and identification of hundreds of microbial pathogens.
Sequence analysis showed unequal base composition for some lineages and substitution saturation at the third codon position (cdp) for all PTLVs similar to that observed by others.
However, analysis of its RNA secondary structure did not indicate a significantly lower free energy than for random sequences with the same base composition, nor did analysis with miRNA prediction programs indicate a miRNA like structure (see Materials).
The average and range (in parentheses) of base composition (percentage) for each data partition across taxa.
Figure 5 shows the average base composition graphs for the three sets.
Analysis of gene size, exon-intron structure and base composition for these 443 predicted genes is summarized in Table 2.
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