2 package "RNAplfold" # don't use package if you're using automake
3 purpose "calculate locally stable secondary structure - pair probabilities"
4 #usage "RNAplfold [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=RNAplfold_cmdl --include-getopt --default-optional --func-name=RNAplfold_cmdline_parser --arg-struct-name=RNAplfold_args_info"
14 description "Computes local pair probabilities for base pairs with a maximal span\
15 of L. The probabilities are averaged over all windows of size L that contain the\
16 base pair. For a sequence of length n and a window size of L the algorithm uses\
17 only O(n+L*L) memory and O(n*L*L) CPU time. Thus it is practical to \"scan\" very\
18 large genomes for short stable RNA structures.\n"
21 section "General Options"
22 sectiondesc="Below are command line options which alter the general behavior of this program\n"
25 "Average the pair probabilities over windows of given size\n\n"
32 "Set the maximum allowed separation of a base pair to span. I.e. no pairs (i,j) with\
33 j-i > span will be allowed. Defaults to winsize if parameter is omitted\n\n"
39 "Report only base pairs with an average probability > cutoff in the dot plot\n\n"
44 option "print_onthefly" o
45 "Save memory by printing out everything during computation.\nNOTE: activated per default for sequences over 1M bp.\n\n"
50 "Compute the mean probability that regions of length 1 to a given length are unpaired.\
51 Output is saved in a _lunp file.\n\n"
57 option "opening_energies" O
58 "Switch output from probabilities to their logarithms, which are NOT exactly the mean\
59 energies needed to the respective stretch of bases!\nNOTE: This actives -u option.\n\n"
63 option "plex_output" -
64 "Create additional output files for RNAplex.\n\n"
70 "Do not automatically substitude nucleotide \"T\" with \"U\"\n\n"
74 section "Model Details"
77 "Rescale energy parameters to a temperature of temp C. Default is 37C.\n\n"
82 "Do not include special tabulated stabilizing energies for tri-, tetra- and hexaloop hairpins. Mostly for testing.\n\n"
87 "How to treat \"dangling end\" energies for bases adjacent to helices in free ends and multi-loops\n"
88 details="With -d2 dangling energies will be added for the bases adjacent to a helix on both sides in\
89 any case.\n\n-d0 ignores dangling ends altogether (mostly for debugging).\n\n"
95 "Produce structures without lonely pairs (helices of length 1).\n"
96 details="For partition function folding this only disallows pairs that can only occur isolated. Other\
97 pairs may still occasionally occur as helices of length 1.\n\n"
102 "Do not allow GU pairs\n\n"
106 option "noClosingGU" -
107 "Do not allow GU pairs at the end of helices\n\n"
112 "Read energy parameters from paramfile, instead of using the default parameter set.\n"
113 details="A sample parameter file should accompany your distribution.\nSee the RNAlib\
114 documentation for details on the file format.\n\n"
120 "Output accessibility profiles in binary format\n."
121 details=" The binary files produced by RNAplfold do not need to be parsed\
122 by RNAplex, so that they are directly loaded into memory. This is useful when large\
123 sequences have to be searched for putative hybridization sites. An other advantage of\
124 the binary format is the 50% file size decrease.\n\n"
129 "Allow other pairs in addition to the usual AU,GC,and GU pairs.\n"
130 details="Its argument is a comma separated list of additionally allowed pairs. If the\
131 first character is a \"-\" then AB will imply that AB and BA are allowed pairs.\ne.g.\
132 RNAfold -nsp -GA will allow GA and AG pairs. Nonstandard pairs are given 0 stacking\
138 option "energyModel" e
139 "Rarely used option to fold sequences from the artificial ABCD... alphabet, where\
140 A pairs B, C-D etc. Use the energy parameters for GC (-e 1) or AU (-e 2) pairs.\n\n"
146 "Set the scaling of the Boltzmann factors\n"
147 details="The argument provided with this option enables to scale the thermodynamic temperature\
148 used in the Boltzmann factors independently from the temperature used to scale the individual\
149 energy contributions of the loop types. The Boltzmann factors then become exp(-dG/(kT*betaScale))\
150 where k is the Boltzmann constant, dG the free energy contribution of the state and T the\
151 absolute temperature.\n\n"
158 text "\nIf in doubt our program is right, nature is at fault.\nComments should be sent to\
159 rna@tbi.univie.ac.at.\n"