The web-server iNuc-PhysChem was developed to identify an uncharacterized DNA sequence as a nucleosome (Figure 1) or linker (non-nucleosome) sequence based on the following 12 physicochemical properties of DNA: (1) A-philicity, (2) base stacking, (3) B-DNA twist, (4) bendability, (5) DNA bending stiffness, (6) DNA denaturation, (7) duplex disrupt energy, (8) duplex free energy, (9) propeller twist, (10) protein deformation, (11) protein-DNA twist and (12) Z-DNA.
Figure 1. A schematic illustration to show the basic architecture of nucleosome. Nucleosomes form the fundamental repeating units of eukaryotic chromatin (upper panel), each of them consists of approximately 147 base pairs of DNA wrapped in 1.67 left-handed superhelical turns around a histone octamer consisting of 2 copies each of the core histones H2A, H2B, H3, and H4 (lower panel).
The anticipated overall success rate is 96.70%, which was derived by the 5-fold cross-validation on the benchmark dataset that can be downloaded from the Data window of this web-server.
(1) For each submission, the number of DNA sequences is limited at 100 or less;
(2) The input sequences must be in FASTA format; i.e., each DNA sequence should start with a greater-than symbol (" > ") in the first column. The words right after the " > " symbol in the single initial line are optional and only used for the purpose of identification and description.
(3) The query DNA sequence should be no shorter than 150 characters. The accepted characters are: A, C, G, T. If a query sequence contains any illegal character, the prediction will be stopped.