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ProbablePair creates a group of suboptimal structures that
contain base pairs above a probability threshold.
USAGE: ProbablePair <pfs file> <ct file> [options]
| <pfs file> |
The name of a file containing base pair probabilities, generated by a partition function calculation. |
| <ct file> |
The name of a CT file to which output will be written.
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| -h, -H, --help |
Display the usage details message. |
| -t, -T, --threshold |
Specify the pairing threshold for pairs to be included.
This should be expressed as a number > 0.5 and <= 1.0.
Default is 0, which signifies structures should be generated
at multiple thresholds: 0.99, 0.97, 0.95, 0.90, 0.80, 0.70,
0.60, and 0.50.
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- Reuter, J.S. and Mathews, D.H.
"RNAstructure: software for RNA secondary structure prediction
and analysis."
BMC Bioinformatics, 11:129. (2010).
- 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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