This finding indicates that this sequence window is a relatively accurate indicator of overall nucleotide variability within and across genotypes M and B (Technical Appendix Figure 1, panels A, C).
This sequence window encompasses one of the known regions containing histone modifications (Chadwick 2008).
Using these sequence features, TSSvote calculated the score of each sequence window by score = 2 δ transcript / EST + δ CpG + δ CAGE + δ H 3 K 4 me 3 + conservation where δ feature equals one if a given feature is located within the sequence window.
Within sequence window sizes from 12 to 20, APCpred final model on homology-reduced dataset achieved an optimal AUC of 0.748 and ACC of 68.43% in fivefold cross-validation at the window size of 20.
If an annotated gene happens to lie within the primary sequence window, the promoter region is shortened to exclude exonic sequence.
This is based on the simple idea that the probability of finding a specific combination of TFBSs within a small sequence window is much smaller (and therefore more significant) than that of finding a single site.
For instance, Capriotti et al. added a description of the amino acid frequency within a symmetrical sequence window centered at the mutated residue and reached a prediction accuracy that was only slightly lower than that achieved using a structurally based approach (Capriotti et al., 2005).
Primer selection was guided by uniqueness of the oligonucleotide sequence across the human genome, as well as the CpG distribution within the 1 Kb sequence window.
PCR primers were designed to amplify approximately 400 600 bp amplicons within a 1 Kb sequence window spanning the sequence represented by the associated microarray feature.
Since our method relies on identifying similar combinations of regulatory signals within the same short sequence window, each runt stripe word profile may not capture the sparse binding sites known to span these CRMs [15].
