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Sequences present at >1% abundance in any sample were clustered by similarity to a seed sequence at 95% identity using UCLUST [26].
This allowed the identification of the nature and orientation of sequences present at the breakpoint relative to the parental chromosome sequences allowing prediction of the structure of the resulting rearranged chromosomes.
We next determined whether genetic evolution may have occurred from the ancestral virus sequences present at baseline in the plasma and/or the PBMCs to the sequences of recently produced viruses found in the plasma and the monocytes during cART.
After the initial sequence selection process, we conducted the research on ten endogenous retroviral loci, all with full LTR sequences, present at least in two primate species and whose phylogeny obey the primate evolutionary history.
The contribution of transcriptional regulatory proteins to the expression of every gene in a genome depends upon the DNA regulatory sequences present at each gene and the physiological environment of the cell.
This occurred for example with strictly identical insertion sequences present at different locations on the analyzed genome.
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Our results showed that all of the 2001 2003 H3 sequences presented at least eight substitutions located at no less than two antigenic sites.
The numbers and percentages of the annotated unique sequences are presented in Additional file 4. In total, 94,535 unique sequences presented at least one significant match in the public databases.
In the presence of two similar sequences with unequal abundance, direct sequencing is relatively insensitive to the sequence present at lower frequency.
We then tested either palindromic sequences derived from the preferential integration sites or the retroviral sequence present at the LTR-LTR junction.
Both possibilities would lead to a lack of correlation between the DBL6ε sequence present at delivery and the specific antibody response.
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