OpenMS
2.6.0
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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/documentation/UTILS_RNADigestor.html Version: 2.6.0 Sep 30 2020, 12:54:34, Revision: c26f752 To cite OpenMS: Rost HL, Sachsenberg T, Aiche S, Bielow C et al.. OpenMS: a flexible open-source software platform for mass spectrometry data analysis. Nat Meth. 2016; 13, 9: 741-748. doi:10.1038/nmeth.3959. 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_U2', 'RNase_A', 'RNase_MC1', 'RNase_H', 'no cleavage', 'unspecific cleavage', 'RNase_T1', 'cusa tivin') -unique Report each unique sequence fragment only once -cdna Input file contains cDNA sequences - replace 'T' with 'U') Common UTIL 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: