| ## RNAstructure Command Line Help partition and partition-smp | ### Contents ### Index
partition is used to calculate the partition function for a sequence, which can be used to predict base pair probabilities. Note that the partition function save file remembers the nucleic acid type it was built with (RNA or DNA), so any further calculations with that file will assume they are done with that same nucleic acid type. The partition function save file, .pfs, is used by other programs to calculate base pairing probabilities (ProbabilityPlot), estimate structures (MaxExpect, ProbKnot), calculate the Shannon entropy (Shannon), or provide the ensemble folding free energy change (EnsembleEnergy). The set of pathways for information flow in available here. partition-smp is a parallel processing version for use on multi-core computers, built using OpenMP. ### USAGE: partition <seq file> <pfs file> [options] ### OR: partition-smp <seq file> <pfs file> [options] ### Required parameters:
<seq file> | The name of a sequence file containing input data. Note that lowercase nucleotides are forced single-stranded in structure prediction.
<pfs file> | The name of a binary partition function save file to which output will be written.
### Options that do not require added values:
-d, -D, --DNA | Specify that the sequence is DNA, and DNA parameters are to be used. Note that this is superseded by --alphabet and that --alphabet DNA also sets DNA parameters. Default is to use RNA parameters.
--disablecoax | Specify that coaxial stacking recusions should not be used. This option uses a less realistic energy function in exchange for a faster calculation.
-h, -H, --help | Display the usage details message.
-i, --isolated | Allow isolated base pairs. The default is to use a heuristic to forbid isolated base pairs. The heuristic prevents pairs (i-j) if (i+1 - j-1) and (i-1 - j+1) pairs are non-canonical pairs.
-q, --quiet | Suppress progress display and other unnecessary output.
-v, --version | Display version and copyright information for this interface.
### Options that require added values:
-a, -A, --alphabet | Specify the name of a folding alphabet and associated nearest neighbor parameters. The alphabet is the prefix for the thermodynamic parameter files, e.g. "rna" for RNA parameters or "dna" for DNA parameters or a custom extended/modified alphabet. The thermodynamic parameters need to reside in the at the location indicated by environment variable DATAPATH. The default is "rna" (i.e. use RNA parameters). This option overrides the --DNA flag. A list of available folding alphabets is here.
-c, -C, --constraint | Specify a folding constraints file to be applied. For partition, 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. Note: The current energy model does not allow base pairs that cannot stack on an adjacent pair, so constraining a single base pair effectively also requires that at least one adjacent pair can be formed. If the resulting PFS file is used to generate a structure (e.g. using MaxExpect) constraining a pair that cannot stack on another pair results in no predicted structure.
-dso, -DSO, --doubleOffset | Specify a double-stranded offset file, which adds energy bonuses to particular double-stranded nucleotides. Default is to have no double-stranded offset specified.
-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.
-sh, -SH, --SHAPE | Specify a SHAPE data file to be used to generate restraints. These restraints specificially use SHAPE pseudoenergy restraints. Default is no SHAPE data file specified.
-si, -SI, --SHAPEintercept | Specify an intercept used with SHAPE restraints. Default is -0.6 kcal/mol.
-sm, -SM, --SHAPEslope | Specify a slope used with SHAPE restraints. Default is 1.8 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.
-x, -X, --experimentalPairBonus | Specify a text file with a two-dimensional matrix of bonuses (in kcal/mol) to apply to each residue pair, as might be obtained from a mutate/map measurement. Matrix must have the same number of rows and columns as the target RNA. Bonus is applied once to edge base pairs, twice to internal base pairs. Default is no experimentalPairBonus file specified.
-xo | Specify an intercept (overall offset) to use with the 2D experimental pairb onus file. Default is 0.0 (no change to input bonuses).
-xs | Specify a number to multiply the 2D experimental pair bonus matrix. Default is 1.0 (no change to input bonuses).
### Notes for smp: partition-smp, by default, will use all available compute cores for processing. The number of cores used can be controlled by setting the OMP_NUM_THREADS environment variable. ### References 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).