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.
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.
- ./RNAConSLOpt -i Example/test.fasta -o Example/test.out
- Benchmarking tests on known riboswitches are available here.
Please contact Shaojie Zhang if you have any suggestions.