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RNAplfold (version 2.1.6.0)

Fasta file:

temperature [°C]:

-T

how to treat dangling end energies:

-d

Average pairing probabilities over this windowsize:

--winsize

Maximum seperation between base pairs:

--span, -L

Cutoff probability for report on base pairing:

--cutoff

Print simplified base pair probabilities (_basepairs output):

--print_onthefly

Output in logarithm of the probabilities (_openen output):

--opening_energies

Compute probabilty that region is unpaired (_lunp output):

advanced options:

RNAplfold

Computes local pair probabilities for base pairs with a maximal span of L. The probabilities are averaged over all windows of size L that contain the base pair. For a sequence of length n and a window size of L the algorithm uses only O(n+L*L) memory and O(n*L*L) CPU time. Thus it is practical to "scan" very large genomes for short stable RNA structures.

Input format

RNAPplfold requires one input file

Fasta file

Outputs

For each structure in the Fasta input a postscript image with dot-plot of the pairing probabilities is generated. Different output is generated with the "--ulength", "--print_onthefly" and "--opening_energies" flags. The Dot Plot Matrices are stored in a Postscript file. The other output is packed in a tar file.