Many enzymes potentially involved in the replication of viral DNA are predicted (Table 3, and EU304328).
Putative genes in the genomic DNA were predicted by means of the software FGENESH [ 91].
Although the M. prima genome encodes more proteins, it is also less gene-dense than other Thermotogales: only 84.6% of its DNA is predicted to be located within protein-coding regions, in contrast to 88 97% in other Thermotogales genomes.
Because the haploid human genome consists of three billion DNA bp, proteins such as Zif268, which bind nine bp of DNA, are predicted to recognize ∼12 000 distinct sites, making single site recognition virtually impossible.
Since continual loss of telomeric DNA is predicted to eventually limit cell proliferation, activation of telomerase in cancer cells may be an important step in the acquisition of cell immortalisation, which occurs during tumour progression (Counter et al, 1998; Meyerson, 2000).
AlkD is a recently discovered bacterial DNA glycosylase that removes positively charged methylpurines from DNA, and was predicted to adopt a protein fold distinct from from those of other DNA repair proteins.
Additionally, during latency, M. tuberculosis continues to be under oxidative stress; thus, the accumulation of mutations caused by oxidative DNA damage was predicted to be a potential risk for drug resistance (Ford et al., 2011).
From the analysis of N = 100 oriented DNA molecules loaded by a single nucleosome (Figure 3C, right panels), we observed some lack of nucleosome positioning from −200 bp to −80 bp upstream the TSS (Figure 3C, left panel), exactly where the DNA molecule was predicted to be intrinsically supercoiled both theoretically (Figure 1) and experimentally (Figure 2).
The efficiency of the amplification was determined from the slope of the least squares fit for each polymerase, and the amount of (E. coli equivalent) rDNA in the zero DNA sample was predicted from the fit equation for each set of serial dilutions.
The origin of chromosomal DNA replication was predicted with the Ori-Finder tool [ 17].
