Compute local minima and energy barriers of a landscape
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.
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
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 (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