2 package "RNApaln" # don't use package if you're using automake
4 purpose "RNA alignment based on sequence base pairing propensities"
6 #usage "RNApaln [options]\n"
8 # Version of your program
9 #version "2.0" # don't use version if you're using automake
12 # command line options passed to gengetopt
13 args "--file-name=RNApaln_cmdl --include-getopt --default-optional --func-name=RNApaln_cmdline_parser --arg-struct-name=RNApaln_args_info"
16 description "Uses string-alignment techniques to perform fast pairwise structural alignments of RNAs.\
17 Similar to RNApdist secondary structure is incorporated in an approximate manner by computing base pair\
18 probabilities, which are then reduced to a vector holding the probability that a base is paired upstream,\
19 downstream, or remains unpaired. Such pair propsensity vectors can then be compared using standard\
20 alignment algorithms. In contrast to RNApdist, RNApaln performs similarity (instead of distance) alignments,\
21 considers both sequence and structure information, and uses affine (rather than linear) gap costs. RNApaln\
22 can perform semi-local alignments by using free end gaps, a true local alignment mode is planned.\n\nThe\
23 same approach has since been used in the StraL program from Gerhard Steeger's group. Since StraL has\
24 optimized parameters and a multiple alignment mode, it be be currently the better option.\n"
27 section "General Options"
28 sectiondesc="Below are command line options which alter the general behavior of this program\n"
30 option "printAlignment" B
31 "Print an \"alignment\" with gaps of the profiles\nThe aligned structures are written\
32 to filename, if specified\nOtherwise output is written to stdout, unless the -Xm option\
33 is set in which case \"backtrack.file\" is used.\n"
34 details="The following symbols are used:\n ( ) essentially upstream (downstream) paired bases\n
35 { } weakly upstream (downstream) paired bases\n | strongly paired bases without preference\n
36 , weakly paired bases without preference\n . essentially unpaired bases.\n\n"
44 "Do not automatically substitude nucleotide \"T\" with \"U\"\n\n"
49 sectiondesc="Select additional algorithms which should be included in the calculations.\n"
52 "Set the alignment mode to be used\n"
53 details="The alignment mode is passed as a single character value. The following options\
54 are available:\n'p' - Compare the structures pairwise, that is first with 2nd, third\
55 with 4th etc. This is the default.\n
56 'm' - Calculate the distance matrix between all structures. The output is formatted\
57 as a lower triangle matrix.\n
58 'f' - Compare each structure to the first one.\n
59 'c' - Compare continuously, that is i-th with (i+1)th structure.\n\n"
65 section "Model Details"
68 "Set the gap open penalty\n\n"
74 "Set the gap extension penalty\n\n"
80 "Set the weight of sequence (compared to structure) in the scoring function.\n\n"
86 "Use free end-gaps\n\n"
91 "Rescale energy parameters to a temperature of temp C. Default is 37C.\n\n"
96 "Do not include special tabulated stabilizing energies for tri-, tetra- and hexaloop hairpins. Mostly for testing.\n\n"
101 "How to treat \"dangling end\" energies for bases adjacent to helices in free ends and multi-loops\n"
102 details="\nWith -d1 only unpaired bases can participate in at most one dangling end, this is the\
103 default for mfe folding but unsupported for the partition function folding.\n\nWith -d2 this check is ignored,\
104 dangling energies will be added for the bases adjacent to a helix on both sides in any case; this is the\
105 default for partition function folding (-p).\nThe option -d0 ignores dangling ends altogether (mostly for\
106 debugging).\nWith -d3 mfe folding will allow coaxial stacking of adjacent helices in multi-loops. At the\
107 moment the implementation will not allow coaxial stacking of the two interior pairs in a loop of degree 3\
108 and works only for mfe folding.\n\nNote that by default (as well as with -d1 and -d3) pf and mfe folding\
109 treat dangling ends differently. Use -d2 in addition to -p to ensure that both algorithms use the same\
116 "Produce structures without lonely pairs (helices of length 1).\n"
117 details="For partition function folding this only disallows pairs that can only occur isolated. Other\
118 pairs may still occasionally occur as helices of length 1.\n\n"
123 "Do not allow GU pairs\n\n"
127 option "noClosingGU" -
128 "Do not allow GU pairs at the end of helices\n\n"
133 "Read energy parameters from paramfile, instead of using the default parameter set.\n"
134 details="A sample parameter file should accompany your distribution.\nSee the RNAlib\
135 documentation for details on the file format.\n\n"
141 "Allow other pairs in addition to the usual AU,GC,and GU pairs.\n"
142 details="Its argument is a comma separated list of additionally allowed pairs. If the\
143 first character is a \"-\" then AB will imply that AB and BA are allowed pairs.\ne.g.\
144 RNAfold -nsp -GA will allow GA and AG pairs. Nonstandard pairs are given 0 stacking\
150 option "energyModel" e
151 "Rarely used option to fold sequences from the artificial ABCD... alphabet, where\
152 A pairs B, C-D etc. Use the energy parameters for GC (-e 1) or AU (-e 2) pairs.\n\n"
157 text "\nIf in doubt our program is right, nature is at fault.\nComments should be sent to\
158 rna@tbi.univie.ac.at.\n"