RNAstructure Predict a Secondary Structure Results

RNAstructure Fold Results
(Predict the lowest free energy structure and a set of low free energy structures for a sequence.)

Command Line:
Fold LtrB_1_to_391_sequence.txt Fold.ct --constraint Folding_constraint_DI_Id1.txt --loop 30 --maximum 5 --percent 10 --SHAPE L550_1_to_391_Na.txt --SHAPEintercept -0.6 --SHAPEslope 2 --temperature 303.15 --window 3

RNAstructure MaxExpect Results
(Generate a structure or structures composed of highly probable base pairs. This is an alternative method for structure prediction that may have higher fidelity in structure prediction.)

Command Line:
MaxExpect partition.pfs MaxExpect.ct --gamma 1 --percent 10 --structures 5 --window 3

RNAstructure ProbKnot Results
(Predict a secondary structure of probable base pairs, which might include pseudoknots.)

Command Line:
ProbKnot partition.pfs ProbKnot.ct --iterations 1 --minimum 3

RNAstructure partition Results
(Perform a partition function calculation on a single sequence to calculate base pair probabilities.)

Command Line:
partition LtrB_1_to_391_sequence.txt partition.pfs --constraint Folding_constraint_DI_Id1.txt --SHAPE L550_1_to_391_Na.txt --SHAPEintercept -0.6 --SHAPEslope 2 --temperature 303.15