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The 719 predicted positions of modification (listed in Additional file 1) from the seven species were mapped onto the universal alignment and then located on secondary structure maps of 16S and 23S rRNA (Figs. 1 and 2).
A novel heteronuclear NMR experiment, HEHAHA, introduced by Jones and Bendiak [ 75], has been used to characterize the primary structures of oligosaccharides as well as to determine positions of modification.
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The comparison of results between the 2 doubly modified structures, with different positions of modifications, confirms that DNA conformational flexibility depends on the presence of particular sequences, and that the neighboring steps influence the conformation adopted by each step.
A natural test statistic is the average relative positioning of modifications within the gene.
For H. volcanii ribosomal RNAs, the type and position of modifications are available in the case of the 16S RNA [ 30, 31], but not for the 23S nor the 5S RNAs.
Positions of histone modification enrichment and protein binding are reported as chromosomal positions, thus areas where the datasets intersect can be determined computationally.
It consists of a list of modified peptides with the following attributes: peptide sequence, measured modification mass and estimated position of the modification along the peptide sequence (modification position).
The properties of the synthesized siRNAs were examined in detail, and it was found that at low concentrations, their silencing abilities were dependent on the positions of the modifications and the types of organic molecules attached.
However, unlike for the E. coli sample, the exact sequence motifs and positions of the modifications are not known.
Many of the more critical and functionally important regions of rRNA are hotspots for guide-target interactions even though the exact positions of methyl modifications are not always conserved (see Figs. 1 and 2).
As discussed in Ewan Birney et al. (2007), assuming Poisson distributed positions of H3K4me2-modifications (as would be needed for an analytic test) gives an unrealistically small variance of the null distribution, and hence leads to false positives.
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