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An RNA secondary structure prediction method that takes co-transcriptional folding into account http://www.e-rna.org/cofold/
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======================================================== ****************** 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: firstname.lastname@example.org 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