Such comprehensive analyses highlighted the behavior of genomic subsystems that may be involved directly or indirectly in S. pyogenes niche adaptation and pathogenesis.
To examine factors influencing the random walk like behavior of genomic DNA sequences, a linear regression model was set up with ZOM, FOM and SOM OUV as response variables to the following predictor variables: growth temperature, AT content, chromosome size, habitat and phyla.
Full-length transcript sequences permit efficient analysis of exon-intron structure and alternative splicing, thus facilitating a complete understanding of the transcriptional behavior of genomic loci [ 5– 7].
The variance tests measuring the random walk like behavior of the genomic DNA sequences are referred to as oligonucleotide usage variance (OUV) [14], [15].
Such genotypic variation was observed long ago in a phenomenon termed phase variation (PV), where frequent genomic changes regulate the phenotypic behavior of the bacteria [ 8].
Two other possible causes for discrepancy exist: intraobserver error, due to subjectivity of the IHC interpretation; and qRT-PCR analysis, which can cause discrepancies particularly in the initial cycles, which depend not only on the melting temperature of the amplicon, but also on the behavior of the genomic vicinity of the amplicon [ 42, 43].
The draft genome sequence of strain BS001 was recently announced (Nazir, Hansen, et al. 2012), but no detail on key genetic systems and on how the genomic information determines the ecophysiological behavior of the organism was provided.
The extensive study of the behavior of the genomic features for experimentally identified protein-protein interactions compared to random protein pairs allowed us to validate the protein-protein interactions adequately.
These results suggest that gene expression at this genomic site is not considerably biased by either the upstream or the downstream genomic elements, and that the neighboring genomic regions do not significantly influence the behavior of pGAL1 and pKlURA.
