Prediction of RNA secondary structure.

: specify the inference engine 

: weight of base pairs 

Prediction of RNA secondary structure by using homologous sequences.

: specify the inference engine for secondary structure 

: specify the inference engine for pairwise alignment 

: weight of base pairs 

: Evalue for homology search against Rfam 

: number of homologous sequences 

Prediction of RNA pseudoknot based on maximizing expected accuracy.

: specify the inference engine 

(NUPACK can be selected only when RNA length is <= 100nt) 

: weight of base pairs (level 2) 

Calculation of energy changes of RNA secondary structures after base mutations.

: maximal span of base pairs 

Calculation of probabilities that each RNA base position is located
within each secondary structural context.

: maximal span of base pairs 

Calculation of of structural accessibility of RNA transcripts.

: maximal span of base pairs 

Validation of RNA secondary structure.
structure.1
predicted by CentroidFold
: weight of base pairs
Your structure (dotbracket format without sequence)
structure.2

Capturing alternative secondary structures of RNA.

: specify the inference engine for canonical structure 

: weight of base pairs 
