# Name of your program
package "RNAfold" # don't use package if you're using automake

purpose "Calculate minimum free energy secondary structures and partition function of RNAs"

#usage "RNAfold [options]\n"
#version "2.0"   # don't use version if you're using automake


# command line options passed to gengetopt
args "--file-name=RNAfold_cmdl --include-getopt --default-optional --func-name=RNAfold_cmdline_parser --arg-struct-name=RNAfold_args_info"


description "The program reads RNA sequences from stdin, calculates their minimum free energy (mfe) structure\
 and prints to stdout the mfe structure in bracket notation and its free energy. If the -p option\
 was given it also computes the partition function (pf) and base pairing probability matrix, and\
 prints the free energy of the thermodynamic ensemble, the frequency of the mfe structure in the ensemble,\
 and the ensemble diversity to stdout.\n\nIt also produces PostScript files with plots of the resulting\
 secondary structure graph and a \"dot plot\" of the base pairing matrix.\nThe dot plot shows a matrix of\
 squares with area proportional to the pairing probability in the upper right half, and one square for each\
 pair in the minimum free energy structure in the lower left half. For each pair i-j with probability\
 p>10E-6 there is a line of the form\n\ni  j  sqrt(p)  ubox\n\nin the PostScript file, so that the pair\
 probabilities can be easily extracted.\n\nSequences may be provided in a simple text format where each sequence\
 occupies a single line. Output files are named \"rna.ps\" and \"dot.ps\". Existing files of the same name\
 will be overwritten.\nIt is also possible to provide sequence data in FASTA format. In this case, the first\
 word (max. 42 char) of the FASTA header will be used for output file names. PostScript files \"name_ss.ps\"\
 and \"name_dp.ps\" are produced for the structure and dot plot, respectively.\nOnce FASTA input was provided\
 all following sequences must be in FASTA format too.\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"

# 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"
flag
off

option  "noconv"  -
"Do not automatically substitude nucleotide \"T\" with \"U\"\n"
flag
off

option  "noPS"  -
"Do not produce postscript drawing of the mfe structure.\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"

option  "partfunc"  p
"Calculate the partition function and base pairing probability matrix.\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-p0 Calculate the partition function but not the pair probabilities,\
 saving about 50% in runtime. This prints the ensemble free energy -kT ln(Z).\n-p2 Compute stack probabilities,\
 i.e. the probability that a pair (i,j) and the immediately interior pair (i+1,j-1) are formed simultaneously in\
 addition to pair probabilities. A second postscript dot plot called \"name_dp2.ps\", or \"dot2.ps\" (if the\
 sequence does not have a name), is produced that contains pair probabilities in the upper right half and stack\
 probabilities in the lower left.\n"
int
default="1"
argoptional
optional

option  "MEA"   -
"Calculate an MEA (maximum expected accuracy) structure, where the expected accuracy is computed from the\
 pair probabilities: each base pair (i,j) gets a score 2*gamma*p_ij and the score of an unpaired base is\
 given by the probability of not forming a pair.\n"
details="The parameter gamma tunes the importance of correctly\
 predicted pairs versus unpaired bases. Thus, for small values of gamma the MEA structure will contain\
 only pairs with very high probability.\nUsing --MEA implies -p for\
 computing the pair probabilities.\n"
float
typestr="gamma"
default="1."
argoptional
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"
double
typestr="scaling factor"
optional
hidden

option  "circ"    c
"Assume a circular (instead of linear) RNA molecule.\n"
flag
off

section "Model Details"

option  "temp"  T
"Rescale energy parameters to a temperature of temp C. Default is 37C.\n"
double
optional

option  "noTetra" 4
"Do not include special tabulated stabilizing energies for tri-, tetra- and hexaloop hairpins. Mostly for testing.\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"
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"
flag
off

option  "noGU"  -
"Do not allow GU pairs\n"
flag
off

option  "noClosingGU" -
"Do not allow GU pairs at the end of helices\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"
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"
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"
int
optional
hidden


text    "References:\n\nThe calculation of mfe structures is based on dynamic programming algorithm originally developed\
 by M. Zuker and P. Stiegler.\nThe partition function algorithm is based on work by J.S. McCaskill.\nThe energy parameters\
 are taken from:\n\nD.H. Mathews, J. Sabina, M. Zuker and H. Turner \"Expanded Sequence Dependence of Thermodynamic\
 Parameters Provides Robust Prediction of RNA Secondary Structure\",  JMB, 288, pp 911-940, 1999\n\nA. Walter, D Turner,\
 J Kim, M Lyttle, P Mueller, D Mathews, M Zuker \"Coaxial stacking of helices enhances binding of oligoribonucleotides.\"\
 PNAS, 91, pp 9218-9222, 1994\n\nIf you use this program in your work you might want to cite:\n\nI.L. Hofacker, W.\
 Fontana, P.F. Stadler, S. Bonhoeffer, M. Tacker, P. Schuster (1994) \"Fast Folding and Comparison of RNA Secondary\
 Structures\", Monatshefte f. Chemie 125: 167-188\n\nM. Zuker, P. Stiegler (1981) \"Optimal computer folding of large RNA\
 sequences using thermodynamic and auxiliary information\", Nucl Acid Res 9: 133-148\n\nJ.S. McCaskill (1990) \"The\
 equilibrium partition function and base pair binding probabilities for RNA secondary structures\", Biopolymers 29:\
 1105-1119\n\nI.L. Hofacker & P.F. Stadler (2006) \"Memory Efficient Folding Algorithms for Circular RNA Secondary\
 Structures\", Bioinformatics\n\nA.F. Bompfuenewerer, R. Backofen, S.H. Bernhart, J. Hertel, I.L. Hofacker, P.F.\
 Stadler, S. Will (2007) \"Variations on {RNA} Folding and Alignment: Lessons from Benasque\", J. Math. Biol.\n\nD. Adams\
 (1979) \"The hitchhiker's guide to the galaxy\", Pan Books, London\n\n"

text    "Written by:\n\nIvo L Hofacker, Walter Fontana, Sebastian Bonhoeffer, Peter F Stadler, Ronny Lorenz.\n\n"
text    "Report bugs:\n\nIf in doubt our program is right, nature is at fault.\nComments should be sent to\
 rna@tbi.univie.ac.at.\n"