Genome profiling (GP) uses a set of DNA fragments sampled from genomic DNAs, and is composed of three fundamental steps: random PCR, micro-temperature gradient gel electrophoresis (μTGGE), and data normalization by computer processing [ 22, 32].
New-sequencing technologies and the dramatic reduction in the cost of sequencing have boosted the development of metagenomics, a new discipline that studies DNA and RNA sequences sampled from genomic material present in a microbial community (Yooseph et al., 2007).
For both the simulated and cell line data sets, the sequencing data analyzed is sampled from genomic regions on a gene-size scale (i.e. tens or hundreds of kbp).
When examining rates of loss, the assumption is made that the duplicates sampled from genomic data are fixed in a population (as well as a constant rate of duplication; see Teufel et al. 2014 for more details on the analysis).
With the development of high-throughput genomic technologies, it has become easy and cost-effective to comprehensively characterize clinical samples by a wide range of genomic data, e.g., depicting cancer samples from epigenomic, genomic and transcriptomic perspectives.
Initially, the RNA was treated with DNase I to clean the samples from any genomic DNA.
Assume we have n samples from the genomic region under consideration (i.e. the control region), and for m<n samples we also have genotype information for a second region (i.e. the coding region).
showed greater genetic diversity at the intergenic spacer locus than did samples from other genomic groups.
Hence, the ratio of keratinocytes to non-keratinocytes in the samples from which genomic DNA was extracted was 18: 11 in (A) and 24: 15 in (B), thus being approximately 4 1 in both cases.
The more ESTs were sampled from a genomic location (sampling depth) the higher is the chance of finding AS events (Supplementary Fig. S2).
