## RNAstructure Command Line Help
PARTS

- ### Contents

- ### Index

PARTS takes two homologous sequences as input and aligns the two sequences and predits base pairing probabilities for conserved structures. It can run in three modes: map (maximum a posteriori) mode to find a maximum probability structure, pp (pair probability) mode, which yields a matrix of base pairing probabilities, or stochsample (stochastic sampling) to sample generated structures.

### USAGE: PARTS <configuration file>

### Required parameters:

<configuration file> | The name of a file containing required configuration data.

### Options that do not require added values:

#### NONE

### Options that require added values:

#### NONE

### Configuration file format:

The following is a description of valid options allowed in the configuration file.

    ################################################################
    # IMPORTANT CONFIG FILE FORMAT NOTES:
    #
    # Config file options described below are case sensitive.
    #
    # Option lines may be specified by the option name followed by a space and the option's desired value.
    # When specifying an option, there may be nothing else on the line.
    # <option> <value>
    #
    # Specifying comment lines:
    # Comment lines must begin with "#" followed by a space.
    # There may not be more than one "#" in a comment line.
    # However, a comment line may be an unbroken string of "#", as in a divider between sets of options.
    #
    # Blank lines are skipped.
    ################################################################

    ################################################################
    # Required input
    ################################################################

    seq1 seq1.seq
    seq2 seq2.seq
    mode map (or pp or stochsample)

    ################################################################
    # Output files; if these aren't specified defaults are used.
    ################################################################

    # Output file for sequence 1 in pp mode
    seq1_pp_op ../my_pp1

    # Output file for sequence 2 in pp mode
    seq2_pp_op my_pp2

    # Output ct for sequence 1 in stochsample mode
    seq1_sample_ct_op ../my_ct1_sample.txt

    # Output ct for sequence 2 in stochsample mode
    seq2_sample_ct_op ../../my_ct2_sample.txt

    # Output alignment file for stochsample mode
    sample_aln_op ./my_aln_sample.txt

    # Output ct for sequence 1 in map mode
    seq1_map_ct_op ../my_map_ct1.txt

    # Output ct for sequence 2 in map mode
    seq2_map_ct_op ../../my_map_ct2.txt

    # Output alignment file for map mode
    map_aln_op ../my_map_aln.txt

    ################################################################
    # Other parameters
    ################################################################

    # Number of structures to sample in stochsample mode
    nsamp 1000

### References:

1. Reuter, J.S. and Mathews, D.H.
   "RNAstructure: software for RNA secondary structure prediction and analysis."
   BMC Bioinformatics, 11:129. (2010).
2. Harmanci, A.O., Sharma, G. and Mathews, D.H.
   "Stochastic sampling of the RNA structural alignment space."
   Nucleic Acids Res., 37:4063-4075. (2009).
3. Harmanci, A.O., Sharma, G. and Mathews, D.H.
   "PARTS: Probabilistic Alignment for RNA joinT Secondary structure prediction."
   Nucleic Acids Res., 36:2406-2417. (2008).