An RNA secondary structure prediction method that takes co-transcriptional folding into account
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Cluster
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Kinfold
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dna_mathews1999.par
dna_mathews2004.par
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rna_andronescu2007.par
rna_turner1999.par
rna_turner2004.par
stamp-h1

README

========================================================
******************      CoFold     *********************
========================================================

ACKNOWLEDGEMENT
===============

The source code of CoFold is derived from the ViennaRNA 2.0.4 package. Full
credit is given Ivo Hofacker's group at the Institute for Theoretical Chemistry
of the University of Vienna.

http://www.tbi.univie.ac.at/RNA/


Note that the file ./lib/naview.c has its own copyright, and it available at
the head of this file. The ./Readseq/ directory contains a modified version of
Don Gilbert's public domain readseq program.



DISCLAIMER AND COPYRIGHT
========== === =========

CoFold is distributed without a warranty of any kind.

Permission to use and generate derivative works of CoFold is granted for
research, education, and commercial purposes, provided that (1) credit is given
to the authors of CoFold at the University of British Columbia and of the
Vienna RNA package at the Institute for Theoretical Chemistry of the University
of Vienna, and that (2) neither CoFold nor its derivative works are distributed
for any fee.


AUTHORS
=======

CoFold is a project undertaken by Jeff R. Proctor and Irmtraud M. Meyer at the
Center for High-Throughput Biology (CHiBi) at the University of British
Columbia. Please contact the authors with queries or comments:

Tel: 1-604-827-4232
Fax: 1-604-822-9126
Email: irmtraud.meyer@cantab.net

Centre for High-Throughput Biology & Department of Computer Science and Department of Medical Genetics
University of British Columbia, 2125 East Mall
Vancouver, BC, V6T 1Z4, Canada


CHANGED FILES
======= =====

Files that have been changed from the Vienna package 2.0.4 source include:
lib/fold.c
Progs/RNAfold.c --> Progs/CoFold.c


DIRECTIONS FOR USE
========== === ===

CoFold modifies the folding routine of the ViennaRNA package, which contains a
wide variety of programs for different purposes. However, CoFold is primarily a
modification of RNAfold, a ViennaRNA tool for calculated the minimum free
energy structure given an input sequence. Purely for practical reasons, the
complete ViennaRNA build system remains as is. when following the installation
instructions, a executable file CoFold will be generated in the Progs
directory.

To build the package:
$ ./configure
$ make

To run CoFold:

$ CoFold [--options]

CoFold accepts an input sequence from standard input, and returns the predicted
structure to standard output. e.g. 'CoFold < myseqfile.fasta'


Parameters unique to CoFold:

        --distAlpha             A value between 0 and 1 for the alpha CoFold model parameter
                                    (optimal value from the authors' training = 0.5) 

        --distTau               A value greater than 0 for the tau CoFold model parameter
                                    (optimal value from the authors' training = 640) 



RNAfold Parameters:



      --noPS                    Do not produce postscript drawing of the mfe 
                                  structure.

      --MEA[=gamma]             Calculate an MEA (maximum expected accuracy) 
                                  structure, where the expected accuracy is 
                                  computed from the pair probabilities: each 
                                  base pair (i,j) gets a score 2*gamma*p_ij and 
                                  the score of an unpaired base is given by the 
                                  probability of not forming a pair.
                                    (default=`1.')
  -p, --partfunc[=INT]          Calculate the partition function and base 
                                  pairing probability matrix.
                                    (default=`1')

  -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')
      --noLP                    Produce structures without lonely pairs 
                                  (helices of length 1).
                                    (default=off)
      --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.
                                Several parameter files are included in this package, 
                                including:
                                rna_andronescu2007.par
                                rna_turner1999.par
                                rna_turner2004.par