DOI: http://dx.doi.org/10.7554/eLife.00348.004 To understand why CGI prediction algorithms often fail, we analysed in detail the nucleotide features of NMIs for all species with a focus on the ratio of observed CpG over expected CpG dinucleotides (CpG O/E) and total G+C nucleotide content (GC content).
Target proteins were distinguished from downstream proteins by labelling the putative target messenger RNA as "seed", which is a 7-nucleotide feature typically found at the 3′-end of an MRE and complementary to the 5′-end of a microRNA.
Four leads containing an adenine scaffold may have implications for targetable inhibitor space in the ATP-binding pocket as they bind with similar or better potency than nucleotides featuring the native phosphate and exocyclic amine.
SVGenes is a pure Ruby language library that allows a user to set styles for tracks of genomic features and will automatically layout and generate SVG images composed of several pre-defined genomics glyphs, including genes, transcripts, data and single-nucleotide features.
For Flaviviridae, we observe an AUC score of 0.70 for the position-based nucleotide frequencies feature set.
From the ΔCcMreBdh co-crystal structures with ADP and AMPPNP, it is clear that the active site could well accommodate a guanidine instead of an adenine as the major contacts are with the ribose and phosphate moieties of the nucleotide, a feature, again, shared with ParM (Gayathri et al., 2013).
Feature fragment density for each TSS is computed as the number of nucleotides with feature over the total number of nucleotides tested.
We recently reported that SV2 binds nucleotides, a feature that has also been reported for another MF family member, the human glucose transporter 1 (Glut1).
A cumulative GC profile was assembled to visualize the general nucleotide composition features of the TvLF.
For each promoter sequence, a vector of size 132, with elements characterizing nucleotide composition features was generated.
