Recent computational methods, such as EP3, which utilizes DNA structure features (e.g., GC content and chemo-physical properties of DNA) [ 28], and CoreBoost_HM, which integrates histone modification information [ 64], have been implemented and have achieved great improvements.
DNA structure features show the lowest correlation across all distance categories, but we found them neither to show consistent directional effects, nor to contribute much to pathogenicity predictions.
Ali et al. also used the DNA composition information, predicted DNA structure, and SNP features, and reported a ~72% accuracy on the human lymphocytes data set using a K nearest neighbor-based classifier [ 12].
Therefore, one DNA strand runs from 5′ → 3′ (five prime to three prime), whereas the other runs from 3′ → 5′. Watson and Crick noted that their proposed DNA structure fulfilled two necessary features of a hereditary molecule.
In particular, TnsE promotes preferential insertion into transferred conjugal DNA using two critical features: DNA structure and specific binding to the sliding β-clamp [25], [34].
Folding of DNA sequences for secondary structure features was with the mFold Web Server: (http://www.bioinformatics.org/sms2/rev_comp.html).org/sms2/rev_comp.html
Aiden's essay, and his related research "creating maps that enable researchers to zoom in on the human genome and reveal features of DNA structure inside the nucleus," has earned him the 2011 GE & Science Prize for Young Life Scientists, the American Association for the Advancement of Science announced Dec. 1.
Long before the basic features of DNA structure and replication were known, the ends of linear eukaryotic chromosomes, called telomeres (literally 'end parts'), were recognized as possessing special properties (Blackburn, 2006).
For a DNA segment, its structure feature was calculated through an empirical formula (Equation 2) proposed by Ponomarenko and his colleagues [ 9, 10].
For each conformational and physicochemical attribute, its x(bjbj+1) values were listed in Additional file 4. Based on Equation 2, for a DNA segment, a structure feature vector was built to represent the TFBS from 38 conformational and physicochemical attributes.
Shanahan et al. [ 19] showed that a protein sequence of known structure and unknown function can be identified as a DNA-binding protein by employing structure features.
