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.)
Download Individual Structures:
Command Line:
Fold sequence.txt Fold.ct --loop 30 --maximum 1000 --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 --gamma 1 --percent 10 --structures 1000 --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 sequence.txt partition.pfs --temperature 310.15