Digests an RNA sequence database in-silico.

pot. predecessor tools	→ RNADigestor →	pot. successor tools
none (FASTA input)	→ RNADigestor →	none (so far)

This application is used to digest an RNA sequence database to get all fragments given a cleavage enzyme.

The command line parameters of this tool are:

RNADigestor -- Digests an RNA sequence database in-silico.
Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_RNADigestor.html
Version: 3.6.0-pre-nightly-2026-04-14 Apr 15 2026, 01:47:25, Revision: daa9562
To cite OpenMS:
 + Pfeuffer, J., Bielow, C., Wein, S. et al.. OpenMS 3 enables reproducible analysis of large-scale mass spec
   trometry data. Nat Methods (2024). doi:10.1038/s41592-024-02197-7.

Usage:
  RNADigestor <options>

Options (mandatory options marked with '*'):
  -in <file>*                 Input file containing RNA sequences (valid formats: 'fasta')
  -out <file>*                Output file containing sequence fragments (valid formats: 'fasta')
  -missed_cleavages <number>  The number of allowed missed cleavages (default: '1') (min: '0')
  -min_length <number>        Minimum length of a fragment (default: '3')
  -max_length <number>        Maximum length of a fragment (default: '30')
  -enzyme <string>            Digestion enzyme (RNase) (default: 'RNase_T1') (valid: 'RNase_A', 'RNase_MC1', 
                              'RNase_H', 'RNase_4', 'RNase_4p', 'RNase_4c', 'mazF', 'RNase_T1_Phosphatase', 
                              'cusativin', 'RNase_U2', 'RNase_T1', 'colicin_E5', 'no cleavage', 'unspecific 
                              cleavage')
  -unique                     Report each unique sequence fragment only once
  -cdna                       Input file contains cDNA sequences - replace 'T' with 'U')
                              
Common TOPP options:
  -ini <file>                 Use the given TOPP INI file
  -threads <n>                Sets the number of threads allowed to be used by the TOPP tool (0 = all availab
                              le cores) (default: '1')
  -write_ini <file>           Writes the default configuration file
  --help                      Shows options
  --helphelp                  Shows all options (including advanced)

INI file documentation of this tool:

Legend:

required parameter

advanced parameter

This section lists all parameters supported by the tool. Parameters are organized into hierarchical subsections that group related settings together. Subsections may contain further subsections or individual parameters.

Each parameter entry contains the following information:

Name The identifier used in configuration files and on the command line.
Default value The value used if the parameter is not explicitly specified.
Description A short explanation describing the purpose and behavior of the parameter.
Tags Additional metadata associated with the parameter.
Restrictions Allowed value ranges for numeric parameters or valid options for string parameters.

Parameter tags provide additional information about how a parameter is used. Some tags indicate whether a parameter is required or intended for advanced configuration, while others may be used internally by OpenMS or workflow tools.

Parameters highlighted as required must be specified for the tool to run successfully. Parameters marked as advanced allow fine-tuning of algorithm behavior and are typically not needed for standard workflows.

+RNADigestorDigests an RNA sequence database in-silico.

version3.6.0-pre-nightly-2026-04-14 Version of the tool that generated this parameters file.

++1Instance '1' section for 'RNADigestor'

in Input file containing RNA sequencesinput file*.fasta

out Output file containing sequence fragmentsoutput file*.fasta

missed_cleavages1 The number of allowed missed cleavages0:∞

min_length3 Minimum length of a fragment

max_length30 Maximum length of a fragment

enzymeRNase_T1 Digestion enzyme (RNase)RNase_A, RNase_MC1, RNase_H, RNase_4, RNase_4p, RNase_4c, mazF, RNase_T1_Phosphatase, cusativin, RNase_U2, RNase_T1, colicin_E5, no cleavage, unspecific cleavage

uniquefalse Report each unique sequence fragment only oncetrue, false

cdnafalse Input file contains cDNA sequences - replace 'T' with 'U')true, false

log Name of log file (created only when specified)

debug0 Sets the debug level

threads1 Sets the number of threads allowed to be used by the TOPP tool (0 = all available cores)

no_progressfalse Disables progress logging to command linetrue, false

forcefalse Overrides tool-specific checkstrue, false

testfalse Enables the test mode (needed for internal use only)true, false