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Fold is used to predict the lowest free energy structure and a set of suboptimal structures, i.e. low free energy structures, using
a variety of constraints.
USAGE: Fold <seq file> <ct file> [options]
| <seq file> |
The name of a file containing an input sequence. Note that lowercase nucleotides are forced single-stranded in structure prediction. |
| <ct file> |
The name of a CT file to which output will be written. |
| -d, -D, --DNA |
Specify that the sequence is DNA, and DNA parameters are to
be used.
Default is to use RNA parameters.
|
| -h, -H, --help |
Display the usage details message. |
| -c, -C, --constraint |
Specify a constraints file to be applied. This can be used to
include folding constraints. For Fold, current supported
constraints are force pairs, force a nucleotide to be single
stranded, and force a nucleotide to be double stranded.
Default is to have no constraints applied.
|
| -l, -L, --loop |
Specify the maximum numbre of unpaired nucleotides in an internal or bulge loop.
Default is 30 unpaired nucleotides.
|
| -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.
|
| -md, -MD, --maxdistance |
Specify a maximum pairing distance; that is, the maximum
number of bases between the two nucleotides in a pair.
Default is no restriction on the distance between pairs.
|
| -p, -P, --percent |
Specify a maximum percent difference in folding free energy
change for generating suboptimal structures.
For example, 20 would indicate 20%.
Default is determined by the length of the sequence.
|
| -s, -S, --save |
Specify the name of a save file, needed for dot plots and
refolding.
Default is not to generate a save file.
|
| -sh, -SH, --SHAPE |
Specify a SHAPE constraints file to be applied. These
constraints specificially use SHAPE pseudoenergy constraints.
Default is no SHAPE constraint file specified.
|
| -si, -SI, --SHAPEintercept |
Specify an intercept used with SHAPE constraints.
Default is -0.8 kcal/mol.
|
| -sm, -SM, --SHAPEslope |
Specify a slope used with SHAPE constraints.
Default is -2.6 kcal/mol.
|
| -t, -T, --temperature |
Specify the temperature at which calculation takes place in
Kelvin.
Default is 310.15 K, which is 37 degrees C.
|
| -w, -W, --window |
Specify a window size.
Default is determined by the length of the sequence.
|
-
Reuter, J.S. and Mathews, D.H.
"RNAstructure: software for RNA secondary structure prediction
and analysis."
BMC Bioinformatics>/i>, 11:129. (2010).
-
Deigan, K.E., Li, T.W., Mathews, D.H. and Weeks, K.M.
"Accurate SHAPE-directed RNA structure determination."
Proc. Natl. Acad. Sci. U.S.A., 106:97-102. (2009).
-
Mathews, D.H., Disney, M.D., Childs, J.L., Schroeder, S.J., Zuker, M. and Turner, D.H.
"Incorporating chemical modification constraints into a dynamic programming algorithm
for prediction of RNA secondary structure."
Proc. Natl. Acad. Sci. USA, 101:7287-7292. (2004).
-
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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