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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>
| <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.
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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).
- 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).
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