--- /dev/null
+# Name of your program
+package "RNAsnoop" # don't use package if you're using automake
+purpose "Find targets of a query H/ACA snoRNA"
+usage "RNAsnoop [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=RNAsnoop_cmdl --include-getopt --default-optional --func-name=RNAsnoop_cmdline_parser --arg-struct-name=RNAsnoop_args_info"
+
+
+description "reads a target RNA sequence and a H/ACA snoRNA sequence
+from a target and query file, respectively and computes optimal
+and suboptimal secondary structures for their hybridization. The
+calculation can be done roughly done in O(nm), where is n the length
+of the target sequence and m is the length of the snoRNA stem, as it
+is specially tailored to the special case of H/ACA snoRNA. For general
+purpose target predictions, please have a look at RNAduplex, RNAup,
+RNAcofold and RNAplex. Accessibility effects can be estimated by
+RNAsnoop if a RNAplfold accessibility profile is provided. \n
+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 '<>' brackets represent snoRNA intramolecular
+interactions, while the '()' brackets represent intermolecular
+interactions between the snoRNA and its target.
+
+The range of the structure in the two sequences in the format
+\"from,to : from,to\"; the energy of duplex structure in
+kcal/mol. If available the opening energy are also returned.\n"
+
+# Options
+section "Input Options"
+sectiondesc="Below are command line options which alter the general input behavior of RNAsnoop\n"
+
+
+option "alignmentLength" L
+"Limit the extent of the interactions to L nucleotides"
+int
+default="25"
+optional
+
+option "constraint" C
+"Calculate the stem structure subject to constraints.\n"
+details="The program reads first the\
+ stem 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 "query" s
+"File containing the query sequence.\n"
+details="Input sequences can be given piped to RNAsnoop or given in a query file with the -s option.\
+ Note that the -s option implies that the -t option is also used\n\n"
+string
+
+option "target" t
+"File containing the target sequence.\n"
+details="Input sequences can be given piped to RNAsnoop or given in a target file with the -t option\
+Note that the -t option implies that the -s option is also used\n\n"
+string
+
+option "suffix" S
+"Specificy the suffix that was added by RNAup to the accessibility files\n\n"
+string
+default="_u1_to_30.out"
+optional
+
+option "from-RNAplfold" P
+"Specify the directory where accessibility profile generated by RNAplfold are found\n\n"
+string
+optional
+
+section "Algorithms"
+sectiondesc="Options which alter the computing behaviour of RNAplex.
+Please note that the options allowing to filter out snoRNA-RNA
+duplexes expect the energy to be given in decacal/mol instead of
+kcal/mol. A threshold of -2.8(kcal/mol) should be given as -280(decacal/mol)\n"
+
+option "alignment-mode" A
+"Specify if RNAsnoop gets alignments or single sequences as input\n\n"
+flag
+off
+
+option "fast-folding" f
+"Speedup of the target search"
+details="This option allows to decide if the backtracking has to be
+done (-f 1) or not (-f 0). For -f 1 the structure is computed based
+on the standard energy model. This is the slowest mode of RNAsnoop. -f
+0 is the fastest mode, as no structure are recomputed and only the
+interaction energy is returned\n\n"
+int
+default="1"
+optional
+
+option "extension-cost" c
+"Cost to add to each nucleotide in a duplex"
+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 (-P option)\n\n"
+int
+default="0"
+optional
+
+option "minimal-right-duplex" o
+"Minimal Right Duplex Energy\n\n"
+default="-270"
+int
+optional
+
+option "minimal-loop-energy" l
+"Minimal Right Duplex Energy\n"
+details="Minimal Stem Loop Energy of the snoRNA. The energy should be
+given in decacalories, i.e. a minimal stem-loop energy of -2.8
+kcal/mol corresponds to -280 decacal/mol\n\n"
+default="-280"
+int
+optional
+
+option "minimal-left-duplex" p
+"Minimal Left Duplex Energy\n\n"
+default="-170"
+int
+optional
+
+option "minimal-duplex" q
+"Minimal Duplex Energy\n\n"
+default="-1090"
+int
+optional
+
+option "duplex-distance" d
+"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. Smaller d leads to larger overlaps between consecutive
+duplexes\n\n"
+int
+default="2"
+optional
+
+option "minimal-stem-length" h
+"Minimal snoRNA stem length\n\n"
+default="5"
+int
+optional
+
+option "maximal-stem-length" i
+"Maximal snoRNA stem length\n\n"
+default="120"
+int
+optional
+
+option "minimal-duplex-box-length" j
+"Minimal distance between the duplex end and the H/ACA box\n\n"
+default="11"
+int
+optional
+
+option "maximal-duplex-box-length" k
+"Maximal distance between the duplex end and the H/ACA box\n\n"
+default="16"
+int
+optional
+
+option "minimal-snoRNA-stem-loop-length" m
+"Minimal number of nucleotides between the beginning of stem loop and
+beginning of the snoRNA sequence\n\n"
+default="1"
+int
+optional
+
+option "maximal-snoRNA-stem-loop-length" n
+"Maximal number of nucleotides between the beginning of stem loop and
+beginning of the snoRNA sequence\n\n"
+default="100000"
+int
+optional
+
+option "minimal-snoRNA-duplex-length" v
+"Minimal distance between duplex start and snoRNA\n\n"
+int
+default="0"
+optional
+
+option "maximal-snoRNA-duplex-length" w
+"Maximal distance between duplex start and snoRNA\n\n"
+int
+default="0"
+optional
+
+option "minimal-duplex-stem-energy" x
+"Minimal duplex stem energy\n\n"
+int
+default="-1370"
+optional
+
+option "minimal-total-energy" y
+"Minimal total energy\n\n"
+int
+default="100000"
+optional
+
+option "maximal-stem-asymmetry" a
+"Maximal snoRNA stem asymmetry\n\n"
+int
+default="30"
+optional
+
+option "minimal-lower-stem-energy" b
+"Minimal lower stem energy\n\n"
+int
+default="100000"
+optional
+
+section "Output options"
+sectiondesc="Options that modifies the output\n\n"
+
+option "energy-threshold" e
+"Maximal energy difference between the mfe and the desired suboptimal\n"
+details="Energy range 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="-1"
+optional
+
+option "produce-ps" I
+"Draw annotated 2D structures for a list of dot-bracket structures\n"
+details="This option allows to produce interaction figures in PS-format with conservation/accessibility annotation, if available\n\n"
+flag
+off
+
+option "output_directory" O
+"Set where the generated figures should be stored\n\n"
+string
+default="./"
+optional
+
+option "direct-redraw" N
+"Outputs 2D interactions concurrently with the interaction calculation for each suboptimal interaction. The -I option should be preferred.\n\n"
+flag
+off
+
+option "from-RNAup" U
+"Specify the directory where accessibility profiles generated by RNAup are found\n\n"
+string
+optional
+
+
+
+
+
+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