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AlignmentPartition and AlignmentPartition-smp

AlignmentPartition is used to calculate the partition function for an alignment of homologous sequence, which can be used to predict base pair probabilities for consensus structures.

AlignmentPartition-smp is a parallel processing version for use on multi-core computers, built using OpenMP.

USAGE: AlignmentPartition <alignment file> <pfs file> [options]

OR: AlignmentPartition-smp <alignment file> <pfs file> [options]

Required parameters:

<alignment file> The name of a file containing an multiple sequence alignment in FASTA format.
Note that lowercase nucleotides are forced single-stranded in structure prediction.
<pfs file> The name of a binary partition function save file to which output will be written.

Options that do not require added values:

--disablecoax Specify that coaxial stacking should not be used in the free energy calculation. This option uses a simpler energy function in exchange for a faster calculation.
-h, -H, --help Display the usage details message.
-v --version Display version and copyright information for this interface.

Options that require added values:

-b -B --bpcutoff Specify the base pairing cutoff.
Default is 0.3
-l -L --loop Specify a maximum internal/bulge loop size.
Default is 40 unpaired nucleotides.

Notes:

AlignmentPartition save files can be used with MaxExpect to estimate structures, ProbabilityPlot to draw plots or provide text files with pair probabilities, or with draw to color annotate predicted structures. Stochastic sampling is not supported at this time.

Notes for smp:

partition-smp, by default, will use all available compute cores for processing. The number of cores used can be controlled by setting the OMP_NUM_THREADS environment variable.

References

  1. Reuter, J.S. and Mathews, D.H.
    "RNAstructure: software for RNA secondary structure prediction and analysis."
    BMC Bioinformatics, 11:129. (2010).
  2. Mathews, D.H.
    "Using an RNA secondary structure partition function to determine confidence in base pairs predicted by free energy minimization."
    RNA, 10:1178-1190. (2004).
  3. McCaskill, J.S.
    "The equilibrium partition function and base pair probabilities for RNA secondary structure."
    Biopolymers, 29:1105-1119. (1990).

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