RNASLOpt

RNASLOpt is a program for predicting stable local optimal secondary structures (represented by stack configurations) for RNAs. RNASLOpt can be used to predict alternate structures for riboswitches.

PLATFORM

Fedora 14

COMPILER

GCC 4.5.1

INSTALLATION

make

DESCRIPTION

USAGE: RNASLOpt -i [infile] -o [outfile] -c [configfile] -d delta -p delta_p -k knum -t barrier_cutoff -l is_onlyLOpt

infile : an input file, each line of which is an RNA sequence.
outfile: an output file, representing all possible local optimal stack configurations and stable local optimal stack configurations ranked according to both free energy and the associated minimal energy barrier.
configfile: optional, the configuration file, by default: Config/config.
delta : optional, only suboptimal structures that within delta kcal/mol of the mfe will be enumerated. Default is 1.
delta_p: optional, only suboptimal structures that within (1-delta_p%) of the mfe will be enumerated. Default is 20%.
knum : optional, the top knum stable local optimal structures will be shown. Default is 5.
barrier_cutoff: optional, the energy barrier cutoff for determining stability of local optimal structures. Default is 12 kcal/mol.
only_LOpt: optional, 1: only LOpt structures are returned. 0: both LOpt and SLOpt structures are returned. Default is 0.

DOWNLOAD

The source code of RNASLOpt is available here.

BENCHMARK RESULTS

The benchmark results of RNASLOpt is available here.

CONTACT US

Please contact Shaojie Zhang if you have any suggestions.