|
bifold is used to predict lowest free energy structures
containing two strands. The structures can contain intramolecular
pairs. A heuristic is used to predict suboptimal structures.
Note that output is written to a CT file where the sequences are
concatenated, with an intermolecular linker between them ("III").
USAGE: bifold <seq file 1> <seq file 2>
<ct file> [options]
| <seq file 1> |
The name of a file containing a first input sequence. Note that lowercase nucleotides are forced single-stranded in structure prediction. |
| <seq file 2> |
The name of a file containing a second 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. Note that the backbone type must be the same for
both sequences.
Default is to use RNA parameters.
|
| -h, -H, --help |
Display the usage details message. |
| -i, -I, --intramolecular |
Forbid intramolecular pairs (pairs within the same strand).
Default is to allow intramolecular pairs.
|
| -l, -L, --loop |
Specify a maximum internal/bulge loop size.
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.
|
| -p, -P, --percent |
Specify a maximum percent energy difference in free energy of
suboptimal structures above the lowest free energy change.
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).
|
| -s, -S, --save |
Specify the name of a save file, needed for dot plots and
refolding.
Default is not to generate a save file.
|
| -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 0 nucleotides.
|
-
Reuter, J.S. and Mathews, D.H.
"RNAstructure: software for RNA secondary structure prediction
and analysis."
BMC Bioinformatics, 11:129. (2010).
-
Mathews, D.H., Burkard, M.E., Freier, S.M., Wyatt, J.R. and
Turner, D.H.
"Predicting oligonucleotide affinity to nucleic acid targets."
RNA, 5:1458-1469. (1999).
|
|
