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General Options: Algorithms: Model Details:%s: cannot dump options to stream %s: `--%s' (`-%c') option given more than once%s %s: `--%s' option given more than once%s %s: invalid numeric value: %s %s: cannot open file for writing: %s %s: option `--%s' doesn't allow an argument %s: option `%c%s' doesn't allow an argument %s: option `%s' requires an argument %s: unrecognized option `--%s' %s: option requires an argument -- %c RNA alignment based on sequence base pairing propensitiesUses 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. The 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. -h, --help Print help and exit --detailed-help Print help, including all details and hidden options, and exit --full-help Print help, including hidden options, and exit -V, --version Print version and exit Below are command line options which alter the general behavior of this program -B, --printAlignment[=filename] Print an "alignment" with gaps of the profiles The aligned structures are written to filename, if specified Otherwise output is written to stdout, unless the -Xm option is set in which case "backtrack.file" is used. (default=`stdout') The following symbols are used: ( ) essentially upstream (downstream) paired bases { } weakly upstream (downstream) paired bases | strongly paired bases without preference , weakly paired bases without preference . essentially unpaired bases. --noconv Do not automatically substitude nucleotide "T" with "U" (default=off) Select additional algorithms which should be included in the calculations. -X, --mode=pmfc Set the alignment mode to be used The alignment mode is passed as a single character value. The following options are available: 'p' - Compare the structures pairwise, that is first with 2nd, third with 4th etc. This is the default. 'm' - Calculate the distance matrix between all structures. The output is formatted as a lower triangle matrix. 'f' - Compare each structure to the first one. 'c' - Compare continuously, that is i-th with (i+1)th structure. --gapo=open Set the gap open penalty --gape=ext Set the gap extension penalty --seqw=w Set the weight of sequence (compared to structure) in the scoring function. --endgaps Use free end-gaps (default=off) -T, --temp=DOUBLE Rescale energy parameters to a temperature of temp C. Default is 37C. -4, --noTetra Do not include special tabulated stabilizing energies for tri-, tetra- and hexaloop hairpins. Mostly for testing. (default=off) -d, --dangles=INT How to treat "dangling end" energies for bases adjacent to helices in free ends and multi-loops (default=`2') With -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. With -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). The option -d0 ignores dangling ends altogether (mostly for debugging). With -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. Note 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. --noLP Produce structures without lonely pairs (helices of length 1). (default=off) For partition function folding this only disallows pairs that can only occur isolated. Other pairs may still occasionally occur as helices of length 1. --noGU Do not allow GU pairs (default=off) --noClosingGU Do not allow GU pairs at the end of helices (default=off) -P, --paramFile=paramfile Read energy parameters from paramfile, instead of using the default parameter set. A sample parameter file should accompany your distribution. See the RNAlib documentation for details on the file format. --nsp=STRING Allow other pairs in addition to the usual AU,GC,and GU pairs. 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. e.g. RNAfold -nsp -GA will allow GA and AG pairs. Nonstandard pairs are given 0 stacking energy. -e, --energyModel=INT 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. References: Bonhoeffer S, McCaskill J S, Stadler P F, Schuster P, (1993), "RNA multi-structure landscapes", Euro Biophys J:22,13-24 Written by: Peter F Stadler, Ivo L Hofacker, Sebastian Bonhoeffer. Report bugs: If in doubt our program is right, nature is at fault. 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