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Barriers

Compute local minima and energy barriers of a landscape

INSTALLATION

Typically, barriers is installed like this:

./configure
./make
./make install

The barriers program uses a large static array for the hash table at the heart of the method. The size of this hash and therefore the maximum size of the landscape you can analyse is set at compile time using the --with-hash-bits option of the ./configure script, e.g.:

./configure --with-hash-bits=27

will create a hash of 2^27 entries.

If you need a hash size >2^27 you may have to set the -mcmodel=medium or -mcmodel=large option in gcc, e.g.:

./configure --with-hash-bits=29 CFLAGS='-mcmodel=medium'

You can use the script perl/get_hashbits.pl to optimize the hashsize given your RAM size and sequence length.

IMPORTANT NOTES

With version 1.7.0, the default move set (-M) for RNA graphs changed from Shift moves to just insertion/removal of single base pairs! To reproduce results obtained with barriers prior to 1.7.0, you need to explicitly activate the Shift move option, e.g.:

barriers -M Shift

PUBLICATIONS

For an explanation of the algorithm, please see

Ch. Flamm, I.L. Hofacker, P.F. Stadler, M.T. Wolfinger. Barrier trees of degenerate landscapes. Z. Phys. Chem., 216:155--173, 2002. doi: 10.1524/zpch.2002.216.2.155

Ligand support has been added with version 1.7.0, see

M.T. Wolfinger, Ch. Flamm, I.L. Hofacker Efficient computation of cotranscriptional RNA-ligand interaction dynamics Methods, 2018 doi: 10.1016/j.ymeth.2018.04.036

COPYRIGHT AND LICENCE

Copyright (C) 2001 Ivo Hofacker, Christoph Flamm, Peter Stadler, Michael T. Wolfinger

barriers is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA

Comments are welcome ivo@tbi.univie.ac.at