RNA secondary structure motif discovery. The standalone version requires the user to provide the input (and eventually background) files in fastB format. Use the encoder provided on the webserver (beam.uniroma2.it/download). ##The executable version is in .jar format (if you want to compile the project by yourself, external libraries (commons.io/math) are not included in the repository. Just add them to the project)
-f input file A fasta file with additional lines for dotbracket (optional) and BEAR encoding (needed). Informally called fastB (fastBEAR).
>ID
primary sequence
dot-bracket
BEAR notation (encodable with the bear Encoder @ http://beam.uniroma2.it/download)
>ID2
...
-g backGround, to compute p-value The background file must have the same format as the input, that is a FASTA file with
>ID
primary sequence
dot-bracket
BEAR notation (encodable with the bear Encoder @ http://beam.uniroma2.it/download)
>ID2
...
-w Min motif Width (10)
-W Max motif Width (50)
-s minSteps (10000)
-S MaxSteps (15000)
-M masks (1) - number of masks(motifs) to be computed
-R runs (1) - number of runs to be tried before choosing the mask
Advanced Options:
-T Starting Temperature (100)
-r cooling Rate (0.001)
-C clean mode (1,2,3) : 1. Exclude negative partials 2. Exclude partials under the 50% of the partial mean 3. Exclude partials under 90% of the mean. (3)
-b f (false) - weight less (mbr[:][:]=0 ) the branch-branch alignments
-v t Verbose, otherwise mostly silent
-k keep all the runs, otherwise show best (for R > 1)
-n model_limit (100) – influences the maximum number of structures that form a motif model. It is advisable not to go over this limit, for computational time reasons. The option is here mostly for developers.
-h print help and exit
Alternative Modes
--circ treat RNAs as if they were circularized (both sequence and structure, and subopts if appliable) you will see a motif that is on the backspliced junction if start and end of a motif position are "switched" (start>end)
awk '/^>/ {print; getline; print; getline; print $1}' <rnafoldOutput> > <encoderReady>
java -jar <encoder.jar> <encoderReady> <BEAMready> then use the <BEAMready> file to run BEAM (-f flag)