NAME

       RNApaln - manual page for RNApaln 2.5.1

SYNOPSIS

       RNApaln [OPTION]...

DESCRIPTION

       RNApaln 2.5.1

       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  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

   General Options:
              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)

   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 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.

   Model Details:
       --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.  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 interior pairs in a loop of degree 3 and works only for mfe folding.

              Note  that  with  -d1  and -d3 only the MFE computations will be using 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 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.

              Different sets  of  energy  parameters  for  RNA  and  DNA  should  accompany  your
              distribution.   See  the  RNAlib documentation for details on the file format. When
              passing the placeholder file name "DNA", DNA parameters are loaded without the need
              to actually specify any input file.

       --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

       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 Structures", 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  modification  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.