RNAstructure Help
NAPSS

NAPSS is used to improve the prediction of an RNA secondary structure by integrating NMR data.

Required parameters:

Options which don't require added values:

NONE

Options which require added values:

NONE

Config file format:

The following example is based on config.txt, a standard example found in the napss directory of the RNAstructure repository.

# The name of the input sequence
inseq=bm.seq

# The name of the input dot plot holding pair probabilities.
indotplot=bm.dp

# The folding constraints file.
inconstraints=bm.con

# The output ct file.
outct=bm.ct

# The pair probabilities file.
outpairs=bm.pp

# The maximum number of tracebacks.
maxtracebacks=1000

# The maximum percent energy difference.
percent=25

# The folding window size.
windowsize=0

# Cutoff percentage range.
cutoff=25
         

1. Reuter, J.S. and Mathews, D.H.
   "RNAstructure: software for RNA secondary structure prediction and analysis."
   BMC Bioinformatics, 11:129. (2010).
2. Hart, J.M., Kennedy, S.D., Mathews, D.H. and Turner, D.H.
   "NMR-assisted prediction of RNA secondary structure: identification of a probable pseudoknot in the coding region of an R2 retrotransposon."
   J. Am. Chem. Soc., 130:10233-10239. (2008).