RNADigestCID can preform theoretical calculations on RNase digested RNA sequences and mass. It can further calculate RNA sequences and mass generated by collision-induced dissociation (CID) in mass spectrometry. The outputs can serve as a reference database for RNA modifications mapping. To run RNADigestCID, 1) install R and run "Rscript Executable.R" in terminal. This script will install required packages and make all R scripts executable ; 2) Create a blank txt file named "FileDirect.txt" in the working directory. The txt will record input file directories.
- Download and save RNA sequences in fasta format.
- Paste fasta file path to the first line of FileDirect.txt.
- In terminal, run: ./RNase( ).R
- The results are precursor ions and will be saved in csv format.
- Paste file path of RNase digested sequences spreadsheet to the second line of FileDirect.txt.
- In terminal, run: ./CID_( ).R
- The results are product ions and will be saved in csv format.
- Paste file path of RNA CID fragmentation spreadsheet to the third line of FileDirect.txt.
- In terminal, run: ./CID_a-B.R
- The results are product ions and will be saved in csv format.
- RNAmod.R uses csv files to calculate mass of the modified precursor and product ions. The second line of FileDirect.txt specifies file path for a RNase digested precursor spreadsheet, and the third line specifies file path for a CID product spreadsheet.
- Specify a modification type in the fourth line of FileDirect.txt using short name symbol from RNAmod_info_Modomics.xml spreadsheet.
- In terminal, run: ./RNAmod.R
- The outputs are in .json format.
- Fasta: Contain two fasta files for testing.
- R: All R scripts for sequences and mass calculations.
- RNAmod_info_Modomics.xml: This spreadsheet contains RNA modification symbols and mass information from Modomics (https://iimcb.genesilico.pl/modomics/modifications).
- RNADigestCID_WorkFlow.pptx: Indicate hierarchy of the codes.