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RNAPALN(1) User Commands RNAPALN(1) NAME RNApaln - manual page for RNApaln 2.7.0 SYNOPSIS RNApaln [OPTION]... DESCRIPTION RNApaln 2.7.0 RNA alignment based on sequence base pairing propensities Uses string-alignment techniques to perform fast pairwise structural alignments of RNAs. Similar to RNApdist secondary structure is incorpo- rated 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 propsen- sity vectors can then be compared using standard alignment algorithms. In contrast to RNApdist, RNApaln performs similarity (instead of dis- tance) 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 -v, --verbose Be verbose. (default=off) Lower the log level setting such that even INFO messages are passed through. I/O Options: Command line options for input and output (pre-)processing -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 substitute nucleotide "T" with "U". (default=off) --log-level=level Set log level threshold. (default=`2') By default, any log messages are filtered such that only warn- ings (level 2) or errors (level 3) are printed. This setting al- lows for specifying the log level threshold, where higher values result in fewer information. Log-level 5 turns off all messages, even errors and other critical information. --log-file[=filename] Print log messages to a file instead of stderr. (default=`RNA- paln.log') --log-time Include time stamp in log messages. (default=off) --log-call Include file and line of log calling function. (default=off) Algorithms: 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 out- put 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 scor- ing function. --endgaps Use free end-gaps (default=off) Energy Parameters: Energy parameter sets can be adapted or loaded from user-pro- vided input files -T, --temp=DOUBLE Rescale energy parameters to a temperature of temp C. Default is 37C. (default=`37.0') -P, --paramFile=paramfile Read energy parameters from paramfile, instead of using the de- fault parameter set. Different sets of energy parameters for RNA and DNA should ac- company your distribution. See the RNAlib documentation for de- tails on the file format. When passing the placeholder file name "DNA", DNA parameters are loaded without the need to actually specify any input file. -4, --noTetra Do not include special tabulated stabilizing energies for tri-, tetra- and hexaloop hairpins. (default=off) Mostly for testing. --salt=DOUBLE Set salt concentration in molar (M). Default is 1.021M. Model Details: Tweak the energy model and pairing rules additionally using the following parameters -d, --dangles=INT How to treat "dangling end" energies for bases adjacent to he- lices in free ends and multi-loops. (default=`2') With -d1 only unpaired bases can participate in at most one dan- gling end. 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 mfe and 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 en- closed pairs in a loop of degree 3 and works only for mfe fold- ing. Note that with -d1 and -d3 only the MFE computations will be us- ing this setting while partition function uses -d2 setting, i.e. dangling ends will be treated differently. --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 oc- cur 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) --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. --energyModel=INT Set energy model. Rarely used option to fold sequences from the artificial ABCD... alphabet, where A pairs B, C-D etc. Use the energy parameters for GC (--energyModel 1) or AU (--energyModel 2) pairs. --helical-rise=FLOAT Set the helical rise of the helix in units of Angstrom. (default=`2.8') Use with caution! This value will be re-set automatically to 3.4 in case DNA parameters are loaded via -P DNA and no further value is provided. --backbone-length=FLOAT Set the average backbone length for looped regions in units of Angstrom. (default=`6.0') Use with caution! This value will be re-set automatically to 6.76 in case DNA parameters are loaded via -P DNA and no further value is provided. REFERENCES If you use this program in your work you might want to cite: R. Lorenz, S.H. Bernhart, C. Hoener zu Siederdissen, H. Tafer, C. Flamm, P.F. Stadler and I.L. Hofacker (2011), "ViennaRNA Package 2.0", Algorithms for Molecular Biology: 6:26 I.L. Hofacker, W. Fontana, P.F. Stadler, S. Bonhoeffer, M. Tacker, P. Schuster (1994), "Fast Folding and Comparison of RNA Secondary Struc- tures", Monatshefte f. Chemie: 125, pp 167-188 R. Lorenz, I.L. Hofacker, P.F. Stadler (2016), "RNA folding with hard and soft constraints", Algorithms for Molecular Biology 11:1 pp 1-13 Bonhoeffer S, McCaskill J S, Stadler P F, Schuster P (1993), "RNA multi-structure landscapes", Euro Biophys J: 22, pp 13-24 The energy parameters are taken from: D.H. Mathews, M.D. Disney, D. Matthew, J.L. Childs, S.J. Schroeder, J. Susan, M. Zuker, D.H. Turner (2004), "Incorporating chemical modifica- tion constraints into a dynamic programming algorithm for prediction of RNA secondary structure", Proc. Natl. Acad. Sci. USA: 101, pp 7287-7292 D.H Turner, D.H. Mathews (2009), "NNDB: The nearest neighbor parameter database for predicting stability of nucleic acid secondary structure", Nucleic Acids Research: 38, pp 280-282 AUTHOR Peter F Stadler, Ivo L Hofacker, Sebastian Bonhoeffer REPORTING BUGS If in doubt our program is right, nature is at fault. Comments should be sent to rna@tbi.univie.ac.at. RNApaln 2.7.0 October 2024 RNAPALN(1)
NAME | SYNOPSIS | DESCRIPTION | REFERENCES | AUTHOR | REPORTING BUGS
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