2 package "RNAplex" # don't use package if you're using automake
3 purpose "Find targets of a query RNA"
4 usage "RNAplex [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=RNAplex_cmdl --include-getopt --default-optional --func-name=RNAplex_cmdline_parser --arg-struct-name=RNAplex_args_info"
14 description "reads two RNA sequences from stdin or <filename> and\
15 computes optimal and suboptimal secondary structures for their\
16 hybridization. The calculation is simplified by allowing only\
17 inter-molecular base pairs. Accessibility effects can be estimated by\
18 RNAplex if a RNAplfold accessibility profile is provided. The\
19 computed optimal and suboptimal structure are written to stdout, one\
20 structure per line. Each line consist of: The structure in dot bracket\
21 format with a \"&\" separating the two strands. The range of the\
22 structure in the two sequences in the format \"from,to : from,to\";\
23 the energy of duplex structure in kcal/mol.\nThe format is especially\
24 useful for computing the hybrid structure between a small probe\
25 sequence and a long target sequence.\n"
28 section "Input Options"
29 sectiondesc="Below are command line options which alter the general input behavior of this program\n"
32 "File containing the query sequence.\n"
33 details="Input sequences can be given piped to RNAplex or given in a query file with the -q option.\
34 Note that the -q option implies that the -t option is also used\n\n"
39 "File containing the target sequence.\n"
40 details="Input sequences can be given piped to RNAplex or given in a target file with the -t option.\
41 Note that the -t option implies that the -q option is also used\n\n"
45 option "accessibility-dir" a
46 "Location of the accessibility profiles.\n"
47 details="This option switches the accessibility modes on and indicates in which directory accessibility\
48 profiles as generated by RNAplfold can be found\n\n"
53 "Allow the reading and parsing of memory dumped opening energy file\n"
54 details="The -b option allows to read and process opening energy files which are saved in binary format\n\
55 This can reduce by a factor of 500x-1000x the time needed to process those files. RNAplex recognizes the\
56 corresponding opening energy files by looking for files named after the sequence and containing the suffix\
57 _openen_bin. Please look at the man page of RNAplfold if you need more information on how to produce binary\
58 opening energy files.\n\n"
63 "Read energy parameters from paramfile, instead of using the default parameter set.\n"
64 details="A sample parameter file should accompany your distribution.\nSee the RNAlib\
65 documentation for details on the file format.\n\n"
71 sectiondesc="Options which alter the computing behaviour of RNAplex.\n"
75 "Rescale energy parameters to a temperature T. Default is 37C.\n\n"
79 option "interaction-length" l
80 "Maximal length of an interaction\n"
81 details="Maximal allowed length of an interaction\n\n"
86 option "extension-cost" c
87 "Cost to add to each nucleotide in a duplex\n"
88 details="Cost of extending a duplex by one nucleotide. Allows to find compact duplexes, having few/small bulges or interior loops\
89 Only useful when no accessibility profiles are available. This option is disabled if accessibility profiles are used (-a option)\n\n"
95 "Compute Tm for probes"
96 details="Use this option if you want to compute the melting temperature of your probes\n\n"
100 option "probe-concentration" Q
101 "Set the probe concentration for the Tm computation\n\n"
106 option "na-concentration" N
107 "Set the Na+ concentration for the Tm computation\n\n"
112 option "mg-concentration" M
113 "Set the Mg2+ concentration for the Tm computation\n\n"
118 option "k-concentration" K
119 "Set the K+ concentration for the Tm computation\n\n"
124 option "tris-concentration" U
125 "Set the tris+ concentration for the Tm computation\n\n"
136 option "fast-folding" f
137 "Speedup of the target search\n"
138 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\
139 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\
140 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\
146 option "scale-accessibility" V
147 "Rescale all opening energy by a factor V\n"
148 details="Scale-factor for the accessibility. If V is set to 1 then the scaling has no effect on the accessibility.\n\n"
153 option "constraint" C
154 "Calculate structures subject to constraints.\n"
155 details="The program reads first the\
156 sequence, then a string containing constraints on the structure for the query sequence encoded with the symbols:\n. (no constraint\
157 for this base)\n| (the corresponding base has to be paired)\n\n"
161 option "alignment-mode" A
162 "Tells RNAplex to compute interactions based on alignments\n"
163 details="If the A option is set RNAplex expects clustalw files as input for the -q and -t option.\n\n"
167 option "convert-to-bin" k
168 "If set, RNAplex will convert all opening energy file in a directory set by the -a option into binary opening energy files\n"
169 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"
174 sectiondesc="Options that modify the output\n"
176 option "duplex-distance" z
177 "Distance between target 3' ends of two consecutive duplexes\n"
178 details="Distance between the target 3'ends of two consecutive duplexes. Should be set to the maximal length of interaction to get\
180 Smaller z leads to larger overlaps between consecutive duplexes.\n\n"
185 option "energy-threshold" e
186 "Minimal energy for a duplex to be returned\n"
187 details="Energy threshold for a duplex to be returned. The threshold is set on the total energy of interaction, i.e. the hybridization\
188 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"
193 option "produce-ps" I
194 "Draw an alignment annotated interaction from RNAplex\n"
195 details="This option allows to produce interaction figures in PS-format a la RNAalifold, where base-pair conservation is represented in\
196 color-coded format. In this mode no interaction are computed, but the -I option indicates the location of the file containing interactions\
197 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"
201 option "WindowLength" L
202 "Tells how large the region around the target site should be for redrawing the alignment interaction\n"
203 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"
209 text "\nIf in doubt our program is right, nature is at fault.\nComments should be sent to\
210 rna@tbi.univie.ac.at.\n"