# Name of your program package "RNAplex" # don't use package if you're using automake purpose "Find targets of a query RNA" usage "RNAplex [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=RNAplex_cmdl --include-getopt --default-optional --func-name=RNAplex_cmdline_parser --arg-struct-name=RNAplex_args_info" description "reads two RNA sequences from stdin or and\ computes optimal and suboptimal secondary structures for their\ hybridization. The calculation is simplified by allowing only\ inter-molecular base pairs. Accessibility effects can be estimated by\ RNAplex if a RNAplfold accessibility profile is provided. The\ computed optimal and suboptimal structure are written to stdout, one\ structure per line. Each line consist of: The structure in dot bracket\ format with a \"&\" separating the two strands. The range of the\ structure in the two sequences in the format \"from,to : from,to\";\ the energy of duplex structure in kcal/mol.\nThe format is especially\ useful for computing the hybrid structure between a small probe\ sequence and a long target sequence.\n" # Options section "Input Options" sectiondesc="Below are command line options which alter the general input behavior of this program\n" option "query" q "File containing the query sequence.\n" details="Input sequences can be given piped to RNAplex or given in a query file with the -q option.\ Note that the -q option implies that the -t option is also used\n\n" string optional option "target" t "File containing the target sequence.\n" details="Input sequences can be given piped to RNAplex or given in a target file with the -t option.\ Note that the -t option implies that the -q option is also used\n\n" string optional option "accessibility-dir" a "Location of the accessibility profiles.\n" details="This option switches the accessibility modes on and indicates in which directory accessibility\ profiles as generated by RNAplfold can be found\n\n" string optional option "binary" b "Allow the reading and parsing of memory dumped opening energy file\n" details="The -b option allows to read and process opening energy files which are saved in binary format\n\ This can reduce by a factor of 500x-1000x the time needed to process those files. RNAplex recognizes the\ corresponding opening energy files by looking for files named after the sequence and containing the suffix\ _openen_bin. Please look at the man page of RNAplfold if you need more information on how to produce binary\ opening energy files.\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 section "Algorithms" sectiondesc="Options which alter the computing behaviour of RNAplex.\n" # Options option "temp" T "Rescale energy parameters to a temperature T. Default is 37C.\n\n" double optional option "interaction-length" l "Maximal length of an interaction\n" details="Maximal allowed length of an interaction\n\n" default="40" int optional option "extension-cost" c "Cost to add to each nucleotide in a duplex\n" details="Cost of extending a duplex by one nucleotide. Allows to find compact duplexes, having few/small bulges or interior loops\ Only useful when no accessibility profiles are available. This option is disabled if accessibility profiles are used (-a option)\n\n" default="0" int optional option "probe-mode" p "Compute Tm for probes" details="Use this option if you want to compute the melting temperature of your probes\n\n" flag off option "probe-concentration" Q "Set the probe concentration for the Tm computation\n\n" double default="0.1" optional option "na-concentration" N "Set the Na+ concentration for the Tm computation\n\n" double default="1.0" optional option "mg-concentration" M "Set the Mg2+ concentration for the Tm computation\n\n" double default="1.0" optional option "k-concentration" K "Set the K+ concentration for the Tm computation\n\n" double default="1.0" optional option "tris-concentration" U "Set the tris+ concentration for the Tm computation\n\n" double default="1.0" optional option "fast-folding" f "Speedup of the target search\n" details="This option allows to decide if the backtracking has to be done (-f 0, -f 2) or not (-f 1). For -f 0 the structure is computed\ based on the standard energy model. This is the slowest and most precise mode of RNAplex. With -f 2, the structure is computed based on the approximated\ plex model. If a lot of targets are returned this is can greatly improve the runtime of RNAplex. -f 1 is the fastest mode, as no structure\ are recomputed \n\n" int default="0" optional option "scale-accessibility" V "Rescale all opening energy by a factor V\n" details="Scale-factor for the accessibility. If V is set to 1 then the scaling has no effect on the accessibility.\n\n" double default="1.0" optional option "constraint" C "Calculate structures subject to constraints.\n" details="The program reads first the\ sequence, then a string containing constraints on the structure for the query sequence encoded with the symbols:\n. (no constraint\ for this base)\n| (the corresponding base has to be paired)\n\n" flag off option "alignment-mode" A "Tells RNAplex to compute interactions based on alignments\n" details="If the A option is set RNAplex expects clustalw files as input for the -q and -t option.\n\n" flag off option "convert-to-bin" k "If set, RNAplex will convert all opening energy file in a directory set by the -a option into binary opening energy files\n" details="RNAplex can be used to convert existing text formatted opening energy files into binary formatted files. In this mode RNAplex does not compute interactions.\n\n" flag off section "Output" sectiondesc="Options that modify the output\n" option "duplex-distance" z "Distance between target 3' ends of two consecutive duplexes\n" details="Distance between the target 3'ends of two consecutive duplexes. Should be set to the maximal length of interaction to get\ good results\n\ Smaller z leads to larger overlaps between consecutive duplexes.\n\n" int default="0" optional option "energy-threshold" e "Minimal energy for a duplex to be returned\n" details="Energy threshold for a duplex to be returned. The threshold is set on the total energy of interaction, i.e. the hybridization\ energy corrected for opening energy if -a is set or the energy corrected by -c. If unset, only the mfe will be returned\n\n" double default="-100000" optional option "produce-ps" I "Draw an alignment annotated interaction from RNAplex\n" details="This option allows to produce interaction figures in PS-format a la RNAalifold, where base-pair conservation is represented in\ color-coded format. In this mode no interaction are computed, but the -I option indicates the location of the file containing interactions\ between two RNA (alignments/sequence) from a previous run. If the -A option is not set a structure figure a la RNAfold with color-coded annotation of the accessibilities is returned\n\n" string optional option "WindowLength" L "Tells how large the region around the target site should be for redrawing the alignment interaction\n" details="This option allow to specify how large the region surrounding the target site should be set when generating the alignment figure of the interaction\n\n" int default="1" optional text "\nIf in doubt our program is right, nature is at fault.\nComments should be sent to\ rna@tbi.univie.ac.at.\n"