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.

RNApaln 2.5.1                                      April 2024                                         RNAPALN(1)