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refold takes a previously folded sequence and can predict a new set of suboptimal structures.
USAGE: refold <save file> <ct file> [options]
| <save file> |
The name of a file containing folding information, generated by Fold.
This file must be a binary folding save file.
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| <ct file> |
The name of a CT file to which output will be written. |
| -h, -H, --help |
Display the usage details message. |
| -m, -M, --maximum |
Specify a maximum number of structures. Note that suboptimal
structures are generated until either the maximum number of
structures are reached or the maximum percent difference is
reached (below).
Default is 20 structures.
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| -p, -P, --percent |
Specify a maximum percent difference in folding free energy
change in suboptimal structures. Note that suboptimal
structures are generated until either the maximum percent
free energy difference is reached or until the maximum number
of structures is reached (above).
Default is 10 percent (specified as 10, not 0.1).
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| -w, -W, --window |
Specify a window size.
Default is determined by the length of the sequence.
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- Reuter, J.S. and Mathews, D.H.
"RNAstructure: software for RNA secondary structure prediction
and analysis."
BMC Bioinformatics>/i>, 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).
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