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MaxExpect

MaxExpect predicts the maximum expected accuracy structure, a structure that maximizes pair probabilities. The paiprobabilities are generated using a partition function calculation.

USAGE: MaxExpect <input file> <ct file> [options]

Required parameters:

<input file> The name of a file containing input data. This input data can be in one of two formats:
  1. Partition function save file (holds base pairing probability data for all pairs and can be generated using the partition interface).
  2. Sequence file (holds raw sequence: .seq or .fasta).
    Note that lowercase nucleotides are forced single-stranded in structure prediction.
    Note that in order to use a squence file, the "sequence" flag must be specified (see "--sequence" below).
<ct file> The name of a CT file to which output will be written.

Options that do not require added values:

-d, -D, --DNA This flag only matters if the input file is a squence file and has been identified as such (see "--sequence" below).
Specify that the sequence is DNA, and DNA parameters are to be used.
Default is to use RNA parameters.
-h, -H, --help Display the usage details message.
--sequence Identify the input file format as a sequence file.

Options that require added values:

-a, -A, --alphabet Specify the name of a folding alphabet and associated nearest neighbor parameters. The alphabet is the prefix for the thermodynamic parameter files, e.g. "rna" for RNA parameters or "dna" for DNA parameters or a custom extended/modified alphabet. The thermodynamic parameters need to reside in the at the location indicated by environment variable DATAPATH.
The default is "rna" (i.e. use RNA parameters). This option overrides the --DNA flag.
-g, -G, --gamma Specify the weight which should be placed on base pairs.
Default is 1.0.
-p, -P, --percent Specify a maximum percent difference in folding free energy change in suboptimal structures. Note that suboptimal structures are generated until either the maximum percent free energy difference is reached or until the maximum number of structures is reached (below).
Default is 50 percent (specified as 50, not 0.5).
-s, -S, --structures Specify a maximum number of structures. Note that suboptimal structures are generated until either the maximum number of structures are reached or the maximum percent difference is reached (above).
Default is 1000 structures.
-w, -W, --window Specify a window size. Smaller windows (down to zero) will result in a larger set of structures that are similar. Larger windows result in fewer structures that are more different in predicted pairs.
Default is 5.

Note:

MaxExpect scores a structure as the sum of pair probabilities for all pairs, multiplied by 2√ógamma, plus the sum of being unpaired for all unpaired nucleotides (see Lu et al.). This score is recorded as an "energy" in CT files, and drawing programs report this as the energy. If a folding free energy is needed, efn2 can be used to calculated it using the nearest neighbor parameters.

References:

  1. Reuter, J.S. and Mathews, D.H.
    "RNAstructure: software for RNA secondary structure prediction and analysis."
    BMC Bioinformatics, 11:129. (2010).
  2. Lu, Z.J., Gloor, J.W. and Mathews, D.H.
    "Improved RNA Secondary Structure Prediction by Maximizing Expected Pair Accuracy."
    RNA, 15:1805-1813. (2009).