YFH and LYC developed and implemented the overall framework and drafted the manuscript; CCH provided valuable suggestion on experiments based on his previous works on predicting DNA-binding residues.
There are several state-of-the-art prediction servers for predicting DNA bindings based on protein sequences, including DISIS [ 2], DNABindR [ 4], BindN [ 5], BindN-rf [ 6], DP-Bind [ 7] and DBS-PRED [ 8].
The structural features of DNA oligomers were defined based on the predicted average 3-dimensional structures of short DNA sequences, which were determined via MD simulations [ 23].
DNA methylation age ('DNAm age') was predicted based on the raw DNA methylation data using the DNA Methylation Age Calculator (https://dnamage.genetics.ucla.edu/ ), as described by Horvath (Horvath S. Genome Biol. 2013 14 R115).
SIDD identifies putative MAR based on the predicted sites of stress-induced DNA duplex destabilisation [ 14].
Based on the DNA and predicted protein sequences analysis of both enzymes, 384 aa (out of 655) of the endochitinase protein showed 95% identity and E value = 0 to a segment of the C terminal region of Chitinase C from Streptomyces albus J1074 (Accession number D6B6V8, Uniprot).
A total of 5 upregulated and 14 downregulated genes were selected based on highest scores for predicted TF binding sites while EMSA band shift assays were carried out with specific antibodies to fully validate the predicted DNA binding activity.
For example, DNA sequence and structure properties are likely to be correlated, because most DNA structures are predicted based on DNA sequences.
Based on standardised predicted FEV1 values.
We established that in wild type hermaphrodites, the interphase X chromosomes are more compact than predicted based on DNA content.
Most transcription factors reported are predicted based on their DNA-binding domain and can be subdivided based on a variety of characteristics such as the number of repeats [ 62].
