# Name of your program package "RNApaln" # don't use package if you're using automake purpose "RNA alignment based on sequence base pairing propensities" #usage "RNApaln [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=RNApaln_cmdl --include-getopt --default-optional --func-name=RNApaln_cmdline_parser --arg-struct-name=RNApaln_args_info" description "Uses string-alignment techniques to perform fast pairwise structural alignments of RNAs.\ Similar to RNApdist secondary structure is incorporated in an approximate manner by computing base pair\ probabilities, which are then reduced to a vector holding the probability that a base is paired upstream,\ downstream, or remains unpaired. Such pair propsensity vectors can then be compared using standard\ alignment algorithms. In contrast to RNApdist, RNApaln performs similarity (instead of distance) alignments,\ considers both sequence and structure information, and uses affine (rather than linear) gap costs. RNApaln\ can perform semi-local alignments by using free end gaps, a true local alignment mode is planned.\n\nThe\ same approach has since been used in the StraL program from Gerhard Steeger's group. Since StraL has\ optimized parameters and a multiple alignment mode, it be be currently the better option.\n" # Options section "General Options" sectiondesc="Below are command line options which alter the general behavior of this program\n" option "printAlignment" B "Print an \"alignment\" with gaps of the profiles\nThe aligned structures are written\ to filename, if specified\nOtherwise output is written to stdout, unless the -Xm option\ is set in which case \"backtrack.file\" is used.\n" details="The following symbols are used:\n ( ) essentially upstream (downstream) paired bases\n { } weakly upstream (downstream) paired bases\n | strongly paired bases without preference\n , weakly paired bases without preference\n . essentially unpaired bases.\n" string default="stdout" typestr="filename" argoptional optional option "noconv" - "Do not automatically substitude nucleotide \"T\" with \"U\"\n" flag off section "Algorithms" sectiondesc="Select additional algorithms which should be included in the calculations.\n" option "mode" X "Set the alignment mode to be used\n" details="The alignment mode is passed as a single character value. The following options\ are available:\n'p' - Compare the structures pairwise, that is first with 2nd, third\ with 4th etc. This is the default.\n 'm' - Calculate the distance matrix between all structures. The output is formatted\ as a lower triangle matrix.\n 'f' - Compare each structure to the first one.\n 'c' - Compare continuously, that is i-th with (i+1)th structure.\n" string typestr="pmfc" optional section "Model Details" option "gapo" - "Set the gap open penalty\n" float typestr="open" optional option "gape" - "Set the gap extension penalty\n" float typestr="ext" optional option "seqw" - "Set the weight of sequence (compared to structure) in the scoring function.\n" float typestr="w" optional option "endgaps" - "Use free end-gaps\n" flag off 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\nBonhoeffer S, McCaskill J S, Stadler P F, Schuster P, (1993), \"RNA multi-structure landscapes\", Euro Biophys J:22,13-24\n\n" text "Written by:\n\nPeter F Stadler, Ivo L Hofacker, Sebastian Bonhoeffer.\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"