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AllSub is used to generate all possible secondary structures
within a small energy increment above the lowest free energy
structure.
USAGE: AllSub <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. |
| -a, -A --absolute |
Specify a maximum absolute energy difference in kcal/mol.
All structures between the lowest free energy and the lowest
free energy plus this parameter will be generated. Note that
suboptimal structures are generated until either the absolute
energy difference is reached or until the maximum percent
energy difference is reached (below).
Default is determined by the length of the sequence.
|
| -c, -C, --constraint |
Specify a constraints file to be applied. This can be used to
include folding constraints. For AllSub, 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.
|
| -p, -P, --percent |
Specify a maximum percent energy difference in folding free
energy change for generating suboptimal structures. All
suboptimal structures are generated at two separate energy
thresholds. The first is the lowest folding free energy. The
second is lowest folding free energy minus a difference
fraction. This difference fraction is calculated by dividing
the percent difference by 100, multiplying that value by the
lowest folding free energy, and subtracting the resultant
value from the lowest folding free energy. Note that
suboptimal structures are generated until either the maximum
percent energy difference is reached or until the absolute
energy difference is reached (above).
Default is determined by the length of the sequence.
|
| -t, -T, --temperature |
Specify the temperature at which calculation takes place in
Kelvin.
Default is 310.15 K, which is 37 degrees C.
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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).
-
Duan, S., Mathews, D.H. and Turner, D.H.
"Interpreting oligonucleotide microarray data to determine RNA
secondary structure: application to the 3' end of Bombyx mori
R2 RNA."
Biochemistry, 45:9819-9832. (2006).
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Wuchty, S., Fontana, W., Hofacker, I.L. and Schuster, P.
"Complete suboptimal folding of RNA and the stability of
secondary structures."
Biopolymers, 49:145-165. (1999).
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