RNADigestor

Digests an RNA sequence database in-silico.

pot. predecessor tools	→ RNADigestor →	pot. successor tools
none (FASTA input)		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/release/3.4.1/html/TOPP_RNADigestor.html
Version: 3.4.1 May 19 2025, 14:24:34, Revision: 8aec8ec
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_4c', 'mazF', 'col
                              icin_E5', 'no cleavage', 'unspecific cleavage', 'cusativin', 'RNase_U2', 'RNase
                              _A', 'RNase_MC1', 'RNase_H', 'RNase_4', 'RNase_4p', 'RNase_T1_Phosphatase', 
                              'RNase_T1')
  -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 (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

+RNADigestorDigests an RNA sequence database in-silico.

version3.4.1 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_4c, mazF, colicin_E5, no cleavage, unspecific cleavage, cusativin, RNase_U2, RNase_A, RNase_MC1, RNase_H, RNase_4, RNase_4p, RNase_T1_Phosphatase, RNase_T1

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

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