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

Bacteria in Bacillus genus used in this study: BacillusBacteria.pdf.
Predicted riboswitch candidates: PredictedRiboswitchCandidates.xls.
Predicted consensus stable local opitmal structures for predicted riboswitch candidates: PredictedStructures.pdf.

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CONTACT US

Please contact Shaojie Zhang if you have any suggestions.