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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]
| <input file> |
The name of a file containing input data. This input
data can be in one of two formats:
- Partition function save file (holds base pairing
probability data for all pairs and can be generated
using the partition
interface).
- 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).
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| <ct file> |
The name of a CT file
to which output will be written. |
| -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. |
| -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. |
MaxExpect scores a structure as the sum of pair probabilities
for all pairs, multiplied by 2×gamma, 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 display this as the energy of a structure. If a folding free energy is
needed, efn2 can be used to calculated
it using the nearest neighbor parameters.
- Reuter, J.S. and Mathews, D.H.
"RNAstructure: software for RNA secondary structure prediction
and analysis."
BMC Bioinformatics, 11:129. (2010).
- 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).
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