RNAConSLOpt
RNAConSLOpt is a program for predicting consensus stable local optimal structures (represented by stack configurations) for aligned RNA sequences. RNAConSLOpt can be used to predict consensus alternate structures for riboswitches.
PLATFORM
Fedora 14
COMPILER
GCC 4.5.1
INSTALLATION
make
DESCRIPTION
USAGE: RNAConSLOpt -i [infile] -o [outfile] -d delta -p percent -t barrier -c [configfile]
- infile : a multiple sequence alignment of related RNAs.
- outfile: an output file, representing all possible consensus local optimal stack configurations and consensus 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 15.
- percent: optional, only suboptimal structures that within (1-delta_p%) of the mfe will be enumerated. Default is 20%.
- barrier: optional, the energy barrier cutoff for determining stability of local optimal structures. Default is 12 kcal/mol.
EXAMPLE
- ./RNAConSLOpt -i Example/test.fasta -o Example/test.out
BENCHMARKS
- Benchmarking tests on known riboswitches are available here.
RIBOSWITCH PREDICTIONS
DOWNLOAD
CONTACT US
Please contact Shaojie Zhang if you have any suggestions.