2 package "RNAsubopt" # don't use package if you're using automake
3 purpose "calculate suboptimal secondary structures of RNAs"
4 #usage "RNAsubopt [options]\n"
6 # Version of your program
7 #version "2.0" # don't use version if you're using automake
10 # command line options passed to gengetopt
11 args "--file-name=RNAsubopt_cmdl --include-getopt --default-optional --func-name=RNAsubopt_cmdline_parser --arg-struct-name=RNAsubopt_args_info"
14 description "reads RNA sequences from stdin and (in the default -e mode) calculates all suboptimal secondary\
15 structures within a user defined energy range above the minimum free energy (mfe). It prints the suboptimal\
16 structures in dot-bracket notation followed by the energy in kcal/mol to stdout. Be careful, the number of\
17 structures returned grows exponentially with both sequence length and energy range.\n\nAlternatively, when\
18 used with the -p option, RNAsubopt produces Boltzmann weighted samples of secondary structures.\n"
22 section "General Options"
23 sectiondesc="Below are command line options which alter the general behavior of this program\n"
26 "Calculate structures subject to constraints.\n"
27 details="The program reads first the\
28 sequence, then a string containing constraints on the structure encoded with the symbols:\n\n. (no constraint\
29 for this base)\n\n| (the corresponding base has to be paired\n\nx (the base is unpaired)\n\n< (base i is paired with\
30 a base j>i)\n\n> (base i is paired with a base j<i)\n\nand matching brackets ( ) (base i pairs base j)\n\nWith the\
31 exception of \"|\", constraints will disallow all pairs conflicting with the constraint. This is usually\
32 sufficient to enforce the constraint, but occasionally a base may stay unpaired in spite of constraints. PF\
33 folding ignores constraints of type \"|\".\n\n"
38 "Do not automatically substitude nucleotide \"T\" with \"U\"\n\n"
43 sectiondesc="Select the algorithms which should be applied to the given RNA sequence.\n"
45 option "deltaEnergy" e
46 "Compute suboptimal structures with energy in a certain range of the optimum (kcal/mol).\
47 Default is calculation of mfe structure only.\n\n"
52 option "deltaEnergyPost" -
53 "Only print structures with energy within range of the mfe after post reevaluation of energies.\n"
54 details="Useful in conjunction with -logML, -d1 or -d3: while the -e option specifies the range\
55 before energies are re-evaluated, this option specifies the maximum energy after re-evaluation.\n\n"
61 "Sort the suboptimal structures by energy.\n"
62 details="Since the sort in is done in memory, this becomes impractical when the number of structures produced\
63 goes into millions. In such cases better pipe the output through \"sort +1n\".\n\n"
68 "Instead of producing all suboptimals in an energy range, produce a random sample of suboptimal structures,\
69 drawn with probabilities equal to their Boltzmann weights via stochastic backtracking in the partition\
70 function. The -e and -p options are mutually exclusive.\n\n"
76 "In the calculation of the pf use scale*mfe as an estimate for the ensemble free energy (used to avoid\
77 overflows). Needed by stochastic backtracking\n"
78 details="The default is 1.07, useful values are 1.0 to 1.2. Occasionally needed\
79 for long sequences.\nYou can also recompile the program to use double precision (see the README file).\n\n"
81 typestr="scaling factor"
86 "Assume a circular (instead of linear) RNA molecule.\n\n"
91 "Compute density of states instead of secondary structures\n"
92 details="This option enables the evaluation of the number of secondary structures in certain energy bands arround\
98 "Compute Zuker suboptimals instead of all suboptimal structures within an engery band arround the MFE.\n\n"
102 section "Model Details"
105 "Rescale energy parameters to a temperature of temp C. Default is 37C.\n\n"
110 "Do not include special tabulated stabilizing energies for tri-, tetra- and hexaloop hairpins. Mostly for testing.\n\n"
115 "How to treat \"dangling end\" energies for bases adjacent to helices in free ends and multi-loops\n"
116 details="\nWith -d1 only unpaired bases can participate in at most one dangling end, this is the\
117 default for mfe folding but unsupported for the partition function folding.\n\nWith -d2 this check is ignored,\
118 dangling energies will be added for the bases adjacent to a helix on both sides in any case; this is the\
119 default for partition function folding (-p).\nThe option -d0 ignores dangling ends altogether (mostly for\
120 debugging).\nWith -d3 mfe folding will allow coaxial stacking of adjacent helices in multi-loops. At the\
121 moment the implementation will not allow coaxial stacking of the two interior pairs in a loop of degree 3\
122 and works only for mfe folding.\n\nNote that by default (as well as with -d1 and -d3) pf and mfe folding\
123 treat dangling ends differently. Use -d2 in addition to -p to ensure that both algorithms use the same\
130 "Produce structures without lonely pairs (helices of length 1).\n"
131 details="For partition function folding this only disallows pairs that can only occur isolated. Other\
132 pairs may still occasionally occur as helices of length 1.\n\n"
137 "Do not allow GU pairs\n\n"
141 option "noClosingGU" -
142 "Do not allow GU pairs at the end of helices\n\n"
147 "Recalculate energies of structures using a logarithmic energy function for multi-loops before output."
148 details="This option does not effect structure generation, only the energies that are printed out.\
149 Since logML lowers energies somewhat, some structures may be missing.\n\n"
154 "Set the scaling of the Boltzmann factors\n"
155 details="The argument provided with this option enables to scale the thermodynamic temperature\
156 used in the Boltzmann factors independently from the temperature used to scale the individual\
157 energy contributions of the loop types. The Boltzmann factors then become exp(-dG/(kT*betaScale))\
158 where k is the Boltzmann constant, dG the free energy contribution of the state and T the\
159 absolute temperature.\n\n"
167 "Read energy parameters from paramfile, instead of using the default parameter set.\n"
168 details="A sample parameter file should accompany your distribution.\nSee the RNAlib\
169 documentation for details on the file format.\n\n"
175 "Allow other pairs in addition to the usual AU,GC,and GU pairs.\n"
176 details="Its argument is a comma separated list of additionally allowed pairs. If the\
177 first character is a \"-\" then AB will imply that AB and BA are allowed pairs.\ne.g.\
178 RNAfold -nsp -GA will allow GA and AG pairs. Nonstandard pairs are given 0 stacking\
184 text "\nIf in doubt our program is right, nature is at fault.\nComments should be sent to\
185 rna@tbi.univie.ac.at.\n"