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In addition, despite the high recombination rate of subtelomeric regions and hence the high expected sequence variability, the majority of genes is conserved between clones (i.e. it is possible to identify pairs or triples of orthologs) as well as their cluster organisation.
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As expected, sequence recovery correlates with ligand displacement.
The oprD gene showed the expected high sequence variability (Figure 6C and Table 4), typical for a gene that is under strong selection for diversity (http://www.pseudomonas.com/related_links.jsp alleles).jsp alleles
Greatest divergence was observed in the comparison between D-loops; as expected considering the considerable sequence variability and difficulty in aligning these regions.
Variations within the recovered HBRV LTR fragments were assessed to check for the sequence variability that is expected from a virus with an error-prone polymerase.
As might be expected, the global post-vaccination data set shows more sequence variability than the Danish pre-/early-vaccination era data set, whereas the latter shows relatively more singletons, i.e. variants present only in a single sequence.
The oprI and oprL genes showed moderate sequence variability comparable to that of housekeeping genes, as could be expected since both genes code for a structural outer membrane lipoprotein (Table 4).
Because PCR was used in an amplification step prior to cloning (unlike the process used for genomic sequencing), it is difficult to discern the expected genetic variability from sequencing error.
As expected, there is no preferential enrichment or loss of any virus sub-population, as detected by sequence variability and prediction of coreceptor tropism.
Based on our sequence variability results, especially with regard to RNA modifications, the accuracy of the sequence-based method is expected to be superior to that of the hybridization-based method.
These peptide-binding sites were expected to have lower levels of conservation because it is well established that the extracellular domains of GPCRs have a large degree of sequence variability.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com