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Remarkably, the major patterns that appeared in the filtered map for complete genomes (Figure 6B) were related to UpA-rich hexanucleotides that produce weak codon-anticodon interactions in coding regions and should hence be under differential selective pressure in both types of sequences.
Both types of sequences reside in all three elements we have defined.
The information acquired from these both types of sequences allows a better characterization of the transgenic cassette.
Some authors emphasize high spatial resolution [ 32, 39] while others prefer high temporal resolution [ 26] and yet again others performed both types of sequences in succession [ 30, 38].
Since the publication by Lukacs et al. [ 29], nomenclature incorporates both types of sequences in the "Z lineage", and newly identified ZE-type loci have been given a "Z" identifier (and not ZE) in their name (eg. [ 34]).
Glutamic acid and serine had the largest enrichment in T4S sequences, whereas isoleucine, tyrosine and glycine were enriched in non-T4S sequences (tryptophan and methionine were not considered because of their low occurrence in both types of sequences).
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Our SNP calls from both types of sequencing libraries correlated very well with the HapMap genotypes on the individual level reflecting the high quality of the SNP calls.
However, in parallel to the steady accumulation of new mt genome data, new nuclear data (e.g., Expressed Sequence Tags – ESTs) need also to be gathered, and only the combination of both types of sequence data might render better results.
In order to test the effect of the homeobox and the repetitive regions in our estimates of nucleotide substitutions, we repeated the previous analyses excluding one or both types of sequence.
They also found that, in left lobe, ADC values are about the same in both types of sequence, supporting the fact that motion artifacts in the left lobe are mostly provoked by cardiac pulse [ 53].
While the constraints on oligonucleotide design described here are good starting points, the optimal constraints to be used to eliminate cross-hybridization from both types of sequence similarity will depend on the genome under investigation and the desired coverage in a given region.
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