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RNAup (version 2.1.6.0)

Fasta file:

temperature [°C]:

-T

how to treat dangling end energies:

-d

Constraints for the secondary structure:

--constraint

Length of the unstructured region.:

--ulength

Specify which contributions to the probabilty of being unpaired are listed in the output:

Maximal length of the region of interaction.:

--window

Include the probability of unpaired regions in both RNAs:

--include_both

Activate pairwise interaction mode:

--interaction_pairwise

Activate pairwise interaction mode, compare always with the first sequence:

--interaction_first

Extend the region of interaction in the target to some residues on the 5' side.:

--extend5

Extend the region of interaction in the target to some residues on the 3' side.:

--extend3

advanced options:

RNAup

RNAup calculates the thermodynamics of RNA−RNA interactions, by decomposing the binding into two stages. (1) First the probability that a potential binding sites remains unpaired (equivalent to the free energy needed to open the site) is computed. (2) Then this accessibility is combined with the interaction energy to obtain the total binding energy. All calculations are done by computing partition functions over all possible conformations.

RNAup provides two different modes: By default RNAup computes accessibilities, in terms of the free energies needed to open a region (default length 4). It prints the region of highest accessibility and its opening energy to stdout, opening energies for all other regions are written to a file.

In interaction mode the interaction between two RNAs is calculated. It is invoked if the input consists of two sequences concatenated with an "&". RNAup assumes that the longer RNA is a structured target sequence while the shorter one is an unstructured small RNA. Additionally, for every position along the target sequence the best free energy of binding for an interaction that includes this position is written to the the output file. Output to stdout consists of the location and free energy, dG, for the optimal region of interaction. The binding energy dG is also split into its components the interaction energy dGint and the opening energy dGu_l (and possibly dGu_s for the shorter sequence). In addition we print the optimal interaction structure as computed by RNAduplex for this region. Note that it can happen that the RNAduplex computed optimal interaction does not coincide with the optimal RNAup region. If the two predictions don’t match the structure string is replaced by a run of ".".

Input format

RNAup requires one input file

Fasta file

For the interaction mode, the sequences of the query and target have to be concatenated by an '&', or the --interaction-pairwise or --interaction-first flags have to be set.

Outputs

most accesible region of each sequence
accesibilties of each sequence is written in a file and these files are bundled together in a tar file