. Author manuscript; available in PMC: 2016 Nov 1.

Published in final edited form as: Nat Protoc. 2015 Oct 1;10(11):1643–1669. doi: 10.1038/nprot.2015.103

Table 4. SuperFold stages and output files.

The initialization stage is executed by the user using the Superfold.py executable. RNAtools.py contains companion classes used by SuperFold. Output directories are named after the input .map file and appended with a hash of the input flags, allowing the user to run multiple jobs within the same directory without encountering conflicting file names. All command line parameters are stored in the log file within the results directory.

Stage	Script/executable	Output files/directories
Initialization	Superfold.py RNAtools.py	results_RNAname_hash/: A results directory with the name of the .map file and a cryptographic hash. All results files will be placed in this directory. log_result*.txt: log file detailing the status of the run.
Partition function calculation	partition (RNAstructure) ProbabilityPlot (RNAstructure) batchSubmit.py	Partition_RNAname_hash/: intermediate files from the windowed partition function calculation will be placed here.
Minimum free-energy (MFE) calculation	Fold (RNAstructure) batchSubmit.py	fold_RNAname_hash/: intermediate files from the MFE calculation will be placed here.
Figure drawing	pvclient.py PyCircleCompare.py drawArcRibbons_simple.py	Analysis files are placed in the results folder: Shannon entropy/SHAPE analysis, partition function arcs, and circle plots and secondary structure diagrams of Shannon entropy/SHAPE regions. Text files for use in a plotting program are also created here.