| ## RNAstructure Command Line Help Shannon | ### Contents ### Index
Shannon calculates the per nucleotide Shannon entropy for secondary structures. The input is a partition function save file, produced by partition. The ouput is a plain text file. ### USAGE: Shannon <pfs file> <text output file> ### Required parameters:
<ct file> | The name of a CT file or Dot-Bracket file containing the input structure.
<energy file> | The energy file to which output is written. The energy file can be written in one of two forms: Simple List Lists free energy for each structure, lowest first. This file type is written by default. Thermodynamic Details Writes details of every substructure in each structure, and corresponding free energy of each. This file type is only written if "-w," "-W," or "--writedetails" (see below) is specified, and replaces a simple list file.
### Notes: The per nucleotide, i, Shannon entropy is the sum (over all possible pairing partners, j) of -Pij log10 (Pij), where Pij is the probability of nucleotides i and j forming a base pair. Note that in some prior work [1,2], the mean was reported across all nucleotides (i). ### References: Mathews, D.H. "Using an RNA secondary structure partition function to determine confidence in base pairs predicted by free energy minimization." RNA, 10:1178. (2004). Huynen, M., Gutell, R., and Konings, D. "Assessing the reliability of RNA folding using statistical mechanics." J. Mol. Biol. 267: 1104. (1997). Reuter, J.S. and Mathews, D.H. "RNAstructure: software for RNA secondary structure prediction and analysis." BMC Bioinformatics, 11:129. (2010).