(45) The rG·dU mismatches were found to be less stable than rG·dT mismatches regardless of neighboring sequence context.
An analysis of neighboring genomic context revealed that gene location within the nucleus is rather dependent on CpG islands, GC content, gene density, and short and long interspersed nuclear elements, collectively known as RIDGE (regions of increased gene expression) properties.
This may reflect influence by neighboring sequence context on overall helical stability and/or propensity to partition into the active site (Li et al., 1996; Yang et al., 1997).
A bias underlying hominid or murine single base polymorphism as determined by neighboring sequence context has been suggested, including effects from nucleotides upwards of 200 bp away from a polymorphic site (Koch 1971; Krawczak et al. 1998; Zhao and Boerwinkle 2002; Zhao and Zhan 2004; Zhang and Zhao 2005).
Cellular automation (CA) calculates cells' changing state through time, based on the state of neighboring cells and context.
These coincident single nucleotide polymorphisms (cSNPs) not only occur significantly more frequently than expected under independence but also cannot be easily explained by natural selection, fine-scale context captured by neighboring nucleotides, or large-scale context captured by GC content (Hodgkinson et al. 2009; Hodgkinson and Eyre-Walker 2010).
Alignment and analysis on 'Maq' was completed in 238 minutes and did not include data on lesion positions with respect to exons, did not display neighboring sequence context, and did not predict amino-acid changes.
To aid the user on the genomic location of the variants and the neighboring genomic context, the resource also features a browser tab displaying the variations on a genome browser interface exported from TBrowse (18).
Notably, the S-signature has moderate coefficients for all 16 trinucleotides related to C → A, implying that among the tobacco-driven C → A mutations, there is no particularly favorable neighboring sequence context.
In order to associate each of the selected subset of human CNE-enhancer with their bona fide target gene, we analyzed the neighboring genomic context using the UCSC [ 55] and Ensembl genome browsers [ 56] and drafted a locus map depicting the flanking genes spanning at least 2 MB interval on either side of CNE-enhancer (Additional file 2: Figure S1).
Whereas TaqMan-based assays are limited by the efficiency of the oligonucleotide probe and dependent on the neighboring nucleotide context, our single-color digital PCR strategy is a highly flexible platform that can be used to interrogate a wide range of genetic targets.
