|
partition-cuda calculates a partition function for a sequence, which can be used to predict base pair probabilities. The code implements a subset of the functionality of partition. It is implemented using CUDA to run on graphical processing units (GPUs).
USAGE: partition-cuda [options] <sequence, or file containing one>
| <seq file> |
The name of a sequence file containing input data or a sequence of composed of all A, C, G, U, and T (uppercase only).
Note that lowercase nucleotides are NOT forced single-stranded in partition-cuda. |
| -d |
Specify that the sequence is DNA, and DNA parameters are to be used.
Default is to use RNA parameters.
|
| -h |
Display the usage details message. |
| -v |
Verbose, i.e. display the dynamic programming algorithm arrays for debugging. |
| -t |
Specify a file to which a matrix of base pairing probabilities will be written. |
| -l |
Specify a file to which -log10 base pairing probabilities will be written. |
| -p |
Specify a ct file name to which the ProbKnot structure will be written. |
| -m |
Specify the minimum helix length for a ProbKnot structure. |
| -b |
Specify a file name from which the thermodynamic parameters will be read. This file is generated by partition-save-params and is in binary format. This can save some startup time as compared to reading the ascii text parameter files, which is the default behavior. |
partition-cuda predicts
base pairing
probabilities. The -log10
base pairing probabilities
data (written using-l) can
be used to color-annotate
predicted structures (see draw)
or generate probaility plots
(see ProbailityPlot). Alternatively,
the program can predict
ProbKnot structures (using
-p), which can contain
pseudoknots. Images can be
made of structures (in ct
format) using draw. If
no file options are chosen,
the program defaults to
outputting the ct for the
ProbKnot structure to
standard out. The number of
CUDA threads is set by a
compile-time variable,
NTHREAD. Two other
compile-time variables
THREAD_X and THREAD_Y set
the dimensions of the block
used for calculations of
internal loops; the product
of these must equal
NTHREAD. By default,
NTHREAD, THREAD_X, and
THREAD_Y are set to 128, 8
and 16, respectively.
- Stern, H.A., and
Mathews, D.H.
"Accelerating calculations of RNA
secondary structure
partition functions using
GPUs."
Algorithms
Mol. Biol., 8:29. (2013).
-
Reuter, J.S., and Mathews, D.H.
"RNAstructure: software for RNA secondary structure prediction and analysis."
BMC Bioinformatics, 11:129. (2010).
- Mathews, D.H.
"Using an RNA secondary structure partition function to determine confidence in base pairs predicted by free energy minimization."
RNA, 10:1178-1190. (2004).
-
McCaskill, J.S.
"The equilibrium partition function and base pair probabilities for RNA secondary structure."
Biopolymers, 29:1105-1119. (1990).
|
