File contents

Program name:
  Rfold

Author:
  Hisanori Kiryu

  Computational Biology Research Center, 
  The National Institute of 
  Advanced Industrial Science and Technology (AIST), Japan.

  E-mail: kiryu-h AT aist.go.jp

License:
  The source files in ./src/vienna/ directory
  contain the energy parameters extracted 
  from the Vienna RNA package (version 1.5) (see Reference below)
  Please follow ./src/vienna/COPYING file,
  which describes the copyright notice of the Vienna RNA package.

  The other part of the source codes is provided as free software.
  They are distributed in the hope that they will be useful
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  

  Permission is granted for research, educational, and commercial use
  and modification so long as 
  1) the package and any derived works are not
     redistributed for any fee, other than media costs, 
  2) proper credit is given to the author and the 
     Computational Biology Research Center, AIST, Japan.
 
  If you want to include this software in a commercial product, please contact 
  the author. 

Citation:
  Rfold: An exact algorithm for computing local base pairing probabilities 
  Hisanori Kiryu; Taishin Kin; Kiyoshi Asai
  Bioinformatics 2007; doi: 10.1093/bioinformatics/btm591

Reference:
  Hofacker, I. (2003) Vienna RNA secondary structure server. 
  Nucleic Acids Res., 31, 342931. 

Install:
  The program was tested using 
  gcc 4.0 on linux machines and gcc 3.4 on cygwin
  Some gcc specific features are currently used.
  
  cd ./src/
  make
  cd ../

Usage:
  run_rfold [options] seqfile

  seqfile: 
    sequence file in fasta format.

  options:
    -command=<COMPUTE_MEA_FOLD|COMPUTE_PROB>
      COMPUTE_MEA_FOLD predicts local secondary structures by using
      the maximal expected accuracy (MEA) method.
      COMPUTE_PROB computes only the base pairing and loop probabilities.
      (default: COMPUTE_MEA_FOLD)
    -max_pair_dist=<integer>
      set the maximal allowed spans W of base pairs.
      set to (-1) for the computation without the constraint on the
      maximal span. (default: -1)
    -outfile=<filename>
      set the output file for structure predictions. (default: rfold_out.txt)
    -mea_outer_loop_coeff=<float>
      compositional weight Co for outer bases. (default: 1.25)
      The compositional weight Cp for base pairs is always set to Cp=1.0
    -mea_inner_outer_ratio=<float>
      set the ratio Ci/Co of the compositional weights Ci, Co for the inner
      and outer unpaired bases, respectively. (default: 0.75)
    -print_prob=<bool>
      set to true in order to print out the base pair probabilities
      when -command=COMPUTE_MEA_FOLD (default: false)
    -print_loop_prob=<bool>
      set to true to print out loop probabilities Prob_L(i) (default: false)
    -prob_file=<filename>
      set output file for base pair and loop probabilities (default: rfold_prob.txt)

Example: 
  ./src/run_rfold -max_pair_dist=30 -print_prob=true ./samples/RNaseP_nuc.fa

Output:
  Both output files for structure predictions and base pairing
  probability computations consist of multiple lines of tab delimited
  columns.
  Sequence positions are represented in 1-based coordinate.

  Structure prediction:
  column 1) start position of the inner region
         2) last position of the inner region
	 3) MEA score of the inner region
         4) secondary structure prediction

    Example (see ./samples/rfold_out.txt):
      #start	end	score	                structure
      10	26	3.529640197753906	<<<<<......>>.>>>
      80	92	2.522617340087891	<<<<.....>>>>
      94	108	3.849872589111328	<<<<<.....>>>>>

  Probability computation:
  column 1) left base position of the base pair
         2) right base position of the base pair
            In the case of loop probabilities columns 1 and 2 are
            identical.
         3) probability value
	 4) probability type: 'P' for base pairing probabilities,
	    'L' for loop probabilities.

     Example (see ./samples/rfold_prob.txt):
       #left_pos  right_pos    prob	        type
       316	  320	       2.0778e-06	P
       313	  317	       3.64299e-05	P
       313	  318	       0.797102	        P
       313	  319	       0.000241128	P
       312	  316	       4.03667e-07	P
       312	  317	       1.05298e-06	P
       312	  318	       9.13579e-05	P

Version History:
  0.1-1 28-January-2008 Changed compile flag to use 'double' numbers
			(rather than 'float') in all the computations.
                        This reduced numerical errors
                        which occasionally produced base pairing probabilities > 1
                        for long (~100kbase) sequences.
  0.1   17-June-2007    Initial Release