RNAstructure Command Line Help: efn2

RNAstructure Command Line Help
efn2 and efn2-smp

ProbScan calculates the exact probability of loops and helices in a structure. Output is written to standard out.

This is a sequence file (.seq or FASTA format) or partition function save file. The default is a partition function save file, the -s flag (below) is used to specify a sequence.

-a -A --hairpin	Print probabilities for all possible hairpin loops.
-b -B --bulge	Print probabilities for all possible bulge loops.
-d -D --DNA	Specify that the sequence is DNA, and DNA parameters are to be used. Default is to use RNA parameters. This only has any effect if a sequence is read and -s is specified.
-h -H --help	Display the usage details message.
--i -I --internal	Print probabilities for all possible internal loops.
-s -S --sequence	Provide a sequence file. Partition function will be calculated (may take a while); if you're going to query the same sequence repeatedly, you could save a lot of time by running from a partition function save file produced by the 'partition' program.
-v -V --version	Display version and copyright information for this interface.

-e -E --helix	Print probabilities for all possible helices with this number of base pair stacks. To get single base pair stacks, use -e 1.
-m -M --multibranch	Provide a file with a list multibranch loops, one multibranch loop per line. Each line should contain a tag followed by a list of pairs where the indices of the pair are separated by a dash and each pair is separated by a tab character; e.g. "loop1 20-40 22-30 32-39" These multibranch loops' probabilities will be checked.
-p -P --pairs	Calculate probability for a user-specified loop. The loop must be provided as a set of pairs of nucleotide indices (1-indexed), where the nucs in the pair are delimited by dashes and each pair is delimited by a comma; eg '-e 5-20' will show the probability of a hairpin loop closed by a pair between nucleotides 5 and 20, and '-e 10-120,15-70,75-110' will give the probability of a three-way junction where the exiting helices are closed by pairs at 10-120, 15-70, and 75-110.

Reuter, J.S. and Mathews, D.H.
"RNAstructure: software for RNA secondary structure prediction and analysis."
BMC Bioinformatics, 11:129. (2010).
Mathews, D.H., Sabina, J., Zuker, M. and Turner, D.H.
"Expanded sequence dependence of thermodynamic parameters provides improved prediction of RNA secondary structure."
J. Mol. Biol., 288:911-940. (1999).