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scorer is used to comparea predicted secondary
structure to an accepted structure. It calculates two quality metrics, sensitivity and PPV (positive predictive value).
USAGE: scorer <predicted ct> <accepted ct>
<output file> [options]
| <predicted ct> |
The name of a file containing predicted structure data in ct format.
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| <accepted ct> |
The name of a file containing accepted structure data in ct format. |
| <output file> |
The name of a text file to which output will be written.
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| -e, -E, --exact |
Specify exact comparison between structures when scoring.
Default is to allow a predicted pair to differ by up to one nucleotide on one side of a pair as compared to the accepted structure. See CircleCompare: exact option" for details.
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| -h, -H, --help |
Display the usage details message. |
| -p, -P, --print |
Print the output file to standard output.
This won't override the default behavior of writing to a
file.
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NONE
- Reuter, J.S. and Mathews, D.H.
"RNAstructure: software for RNA secondary structure prediction
and analysis."
BMC Bioinformatics, 11:129. (2010).
- Mathews, D.H., Sabina, J., Zuker, M. and Turner, D.H.
"Expanded sequence dependence of thermodynamic parameters provides improved prediction
of RNA secondary structure."
J. Mol. Biol., 288:911-940. (1999).
- Mathews, D.H.
"Using an RNA secondary structure partition function to
determine confidence in base pairs predicted by free
energy minimization."
RNA, 10:1178-1190. (2004).
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