|
bipartition is used to predict the partition function for
structures containing two strands. Note that the structures do
not include those with intramolecular pairs.
Note that output is written to a partition function save file
where the sequences are concatenated, with an intermolecular
linker between them ("III").
USAGE: bipartition <seq file 1> <seq file 2>
<pfs 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. |
| <pfs file> |
The name of a partition function save 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. |
| -t, -T, --temperature |
Specify the temperature at which calculation takes place in
Kelvin.
Default is 310.15 K, which is 37 degrees C.
|
-
Reuter, J.S. and Mathews, D.H.
"RNAstructure: software for RNA secondary structure prediction
and analysis."
BMC Bioinformatics, 11:129. (2010).
-
Lu, Z.J. and Mathews, D.H.
"Efficient siRNA Selection Using Hybridization Thermodynamics."
Nucleic Acids Res., 36:640-647. (2007).
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