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 Predict1.fasta Fold.ct --DNA --loop 30 --maximum 20 --percent 10 --temperature 310.15 --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 --DNA --gamma 1 --percent 10 --structures 20 --window 3

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

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

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

Command Line:
partition Predict1.fasta partition.pfs --DNA --temperature 310.15