--- /dev/null
+# Name of your program
+package "RNAcofold" # don't use package if you're using automake
+
+purpose "calculate secondary structures of two RNAs with dimerization"
+
+#usage "RNAcofold [options]\n"
+# Version of your program
+#version "2.0" # don't use version if you're using automake
+
+
+# command line options passed to gengetopt
+args "--file-name=RNAcofold_cmdl --include-getopt --default-optional --func-name=RNAcofold_cmdline_parser --arg-struct-name=RNAcofold_args_info"
+
+
+description "The program works much like RNAfold, but allows to specify two RNA sequences wich are\
+ then allowed to form a dimer structure. RNA sequences are read from stdin in the usual\
+ format, i.e. each line of input corresponds to one sequence, except for lines starting\
+ with \">\" which contain the name of the next sequence.\nTo compute the hybrid structure\
+ of two molecules, the two sequences must be concatenated using the \'&\' character as\
+ separator.\nRNAcofold can compute minimum free energy (mfe) structures, as well as\
+ partition function (pf) and base pairing probability matrix (using the -p switch)\nSince\
+ dimer formation is concentration dependent, RNAcofold can be used to compute equilibrium\
+ concentrations for all five monomer and (homo/hetero)-dimer species, given input\
+ concentrations for the monomers.\nOutput consists of the mfe structure in bracket\
+ notation as well as PostScript structure plots and \"dot plot\" files containing the\
+ pair probabilities, see the RNAfold man page for details. In the dot plots a cross marks\
+ the chain break between the two concatenated sequences.\nThe program will continue to\
+ read new sequences until a line consisting of the single character @ or an end of file\
+ condition is encountered.\n\n"
+
+# Options
+section "General Options"
+sectiondesc="Below are command line options which alter the general behavior of this program\n"
+
+option "constraint" C
+"Calculate structures subject to constraints.\n"
+details="The program reads first the\
+ sequence, then a string containing constraints on the structure encoded with the symbols:\n\n. (no constraint\
+ 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\
+ 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\
+ exception of \"|\", constraints will disallow all pairs conflicting with the constraint. This is usually\
+ sufficient to enforce the constraint, but occasionally a base may stay unpaired in spite of constraints. PF\
+ folding ignores constraints of type \"|\".\n\n"
+flag
+off
+
+option "noconv" -
+"Do not automatically substitude nucleotide \"T\" with \"U\"\n\n"
+flag
+off
+
+option "noPS" -
+"Do not produce postscript output\n\n"
+flag
+off
+
+section "Algorithms"
+sectiondesc="Select additional algorithms which should be included in the calculations.\nThe Minimum free energy\
+ (MFE) and a structure representative are calculated in any case.\n\n"
+
+option "partfunc" p
+"Calculate the partition function and base pairing probability matrix in\
+ addition to the mfe structure. Default is calculation of mfe structure only.\n"
+details="In addition to the MFE structure\
+ we print a coarse representation of the pair probabilities in form of a pseudo bracket notation, followed by\
+ the ensemble free energy, as well as the centroid structure derived from the pair probabilities together with\
+ its free energy and distance to the ensemble. Finally it prints the frequency of the mfe structure, and the\
+ structural diversity (mean distance between the structures in the ensemble).\nSee the description of pf_fold()\
+ and mean_bp_dist() and centroid() in the RNAlib documentation for details.\nNote that unless you also specify\
+ -d2 or -d0, the partition function and mfe calculations will use a slightly different energy model. See the\
+ discussion of dangling end options below.\n\nAn additionally passed value to this option changes the behavior\
+ of partition function calculation:\n\n\
+ In order to calculate the partition function but not the pair probabilities use the -p0 option and save about
+ 50% in runtime. This prints the ensemble free energy -kT ln(Z).\n\n"
+int
+default="1"
+argoptional
+optional
+
+option "all_pf" a
+"Compute the partition function and free energies not only of the hetero-dimer consisting\
+ of the two input sequences (the \"AB dimer\"), but also of the homo-dimers AA and BB as\
+ well as A and B monomers.\n"
+details="The output will contain the free energies for each of these species, as well as\
+ 5 dot plots containing the conditional pair probabilities, called ABname5.ps, AAname5.ps\
+ and so on. For later use, these dot plot files also contain the free energy of the\
+ ensemble as a comment. Using -a automatically toggles the -p option.\n\n"
+flag
+off
+
+option "concentrations" c
+"In addition to everything listed under the -a option, read in initial monomer concentrations\
+ and compute the expected equilibrium concentrations of the 5 possible species (AB, AA, BB, A, B).\n"
+details="Start concentrations are read from stdin (unless the -f option is used) in [mol/l],\
+ equilibrium concentrations are given realtive to the sum of the two inputs. An arbitrary number\
+ of initial concentrations can be specified (one pair of concentrations per line).\n\n"
+flag
+off
+
+option "concfile" f
+"Specify a file with initial concentrations for the to sequences."
+details="The table consits of arbitrary many lines with just two numbers (the concentration of\
+ sequence A and B). This option will automatically toggle the -c (and thus -a and -p) options (see above).\n\n"
+string
+typestr="filename"
+optional
+
+option "pfScale" S
+"In the calculation of the pf use scale*mfe as an estimate for the ensemble free energy (used to avoid\
+ overflows).\n"
+details="The default is 1.07, useful values are 1.0 to 1.2. Occasionally needed\
+ for long sequences.\nYou can also recompile the program to use double precision (see the README file).\n\n"
+double
+typestr="scaling factor"
+optional
+hidden
+
+option "bppmThreshold" -
+"Set the threshold for base pair probabilities included in the postscript output\n"
+details="By setting the threshold the base pair probabilities that are included in the\
+ output can be varied. By default only those exceeding 1e-5 in probability will be shown as squares\
+ in the dot plot. Changing the threshold to any other value allows for increase or decrease of data.\n\n"
+double
+typestr="<value>"
+optional
+default="1e-5"
+hidden
+
+option "gquad" g
+"Incoorporate G-Quadruplex formation into the structure prediction algorithm\n"
+flag
+off
+
+section "Model Details"
+
+option "temp" T
+"Rescale energy parameters to a temperature of temp C. Default is 37C.\n\n"
+double
+
+option "noTetra" 4
+"Do not include special stabilizing energies for certain tetra-loops. Mostly for testing.\n\n"
+flag
+off
+
+option "dangles" d
+"How to treat \"dangling end\" energies for bases adjacent to helices in free ends and multi-loops\n"
+details="\nWith -d1 only unpaired bases can participate in at most one dangling end, this is the\
+ default for mfe folding but unsupported for the partition function folding.\n\nWith -d2 this check is ignored,\
+ dangling energies will be added for the bases adjacent to a helix on both sides in any case; this is the\
+ default for partition function folding (-p).\nThe option -d0 ignores dangling ends altogether (mostly for\
+ debugging).\nWith -d3 mfe folding will allow coaxial stacking of adjacent helices in multi-loops. At the\
+ moment the implementation will not allow coaxial stacking of the two interior pairs in a loop of degree 3\
+ and works only for mfe folding.\n\nNote that by default (as well as with -d1 and -d3) pf and mfe folding\
+ treat dangling ends differently. Use -d2 in addition to -p to ensure that both algorithms use the same\
+ energy model.\n\n"
+int
+default="2"
+optional
+
+option "noLP" -
+"Produce structures without lonely pairs (helices of length 1).\n"
+details="For partition function folding this only disallows pairs that can only occur isolated. Other\
+ pairs may still occasionally occur as helices of length 1.\n\n"
+flag
+off
+
+option "noGU" -
+"Do not allow GU pairs\n\n"
+flag
+off
+
+option "noClosingGU" -
+"Do not allow GU pairs at the end of helices\n\n"
+flag
+off
+
+option "paramFile" P
+"Read energy parameters from paramfile, instead of using the default parameter set.\n"
+details="A sample parameter file should accompany your distribution.\nSee the RNAlib\
+ documentation for details on the file format.\n\n"
+string
+typestr="paramfile"
+optional
+
+option "nsp" -
+"Allow other pairs in addition to the usual AU,GC,and GU pairs.\n"
+details="Its argument is a comma separated list of additionally allowed pairs. If the\
+ first character is a \"-\" then AB will imply that AB and BA are allowed pairs.\ne.g.\
+ RNAfold -nsp -GA will allow GA and AG pairs. Nonstandard pairs are given 0 stacking\
+ energy.\n\n"
+string
+optional
+hidden
+
+option "energyModel" e
+"Rarely used option to fold sequences from the artificial ABCD... alphabet, where\
+ A pairs B, C-D etc. Use the energy parameters for GC (-e 1) or AU (-e 2) pairs.\n\n"
+int
+optional
+hidden
+
+option "betaScale" -
+"Set the scaling of the Boltzmann factors\n"
+details="The argument provided with this option enables to scale the thermodynamic temperature\
+ used in the Boltzmann factors independently from the temperature used to scale the individual\
+ energy contributions of the loop types. The Boltzmann factors then become exp(-dG/(kT*betaScale))\
+ where k is the Boltzmann constant, dG the free energy contribution of the state and T the\
+ absolute temperature.\n\n"
+double
+default="1."
+optional
+hidden
+
+text "\nIf in doubt our program is right, nature is at fault.\nComments should be sent to\
+ rna@tbi.univie.ac.at.\n"
git://source.jalview.org / jabaws.git / blobdiff