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RNAsubopt (version 2.1.6.0)

Fasta file:

temperature [°C]:

-T

how to treat dangling end energies:

-d

Constraints for the secondary structure:

--constraint

Sort the secondary structures by energy:

--sorted

Calculate the density of states instead of the structure:

--dos

Calculate the Zuker suboptimals instead of the structures within a range.:

--zuker

select algorithm:

Range of energy for the suboptimal structures.:

--deltaEnergy

select output restriction:

advanced options:

RNAsubopt

In the default -e mode RNAsubopt calculates all suboptimal secondary structures within a user defined energy range above the minimum free energy (mfe). It prints the suboptimal structures in dot-bracket notation followed by the energy in kcal/mol to stdout. Be careful, the number of structures returned grows exponentially with both sequence length and energy range.

Alternatively, when used with the -p option, RNAsubopt produces Boltzmann weighted samples of secondary structures.

Input format

RNAsubopt requires one input file

fasta file

Outputs

secondary structure in dot-bracket format