## RNAstructure Command Line Help
Multifind

- ### Contents

- ### Index

Multifind uses multilign, which predicts common structures for multiple homologous sequences, and estimates the probability that the input sequences are a conserved non-coding RNA using a classification support vector machine. It has two distinct executables, a serial program called Multifind and a parallelized program called Multifind-smp for use in shared memory enviroments.

### USAGE 1: Multifind <configuration file>

### USAGE 1: Multifind-smp <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.
The example is based on Multifind_sample.conf, a standard example found in the examples directory of the RNAstructure repository.

    ################################################################
    # IMPORTANT CONFIG FILE FORMAT NOTES:
    #
    # Config file options described below are not case sensitive.
    #
    # Option lines may be specified by the option name followed by an equals sign and the option's desired value.
    # When specifying an option, there may be nothing else on the line.
    # If an option is specified more than once, the last specification is used.
    # <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.
    # Any leading or trailing whitespace is ignored.
    # Variables may not contain internal whitespace.
    #
    # Syntax errors produce a warning to standard output and are then ignored.
    ################################################################

    ################################################################
    # Input options.
    # If an appropriate group of these values is not defined, the program will exit.
    ################################################################

    #Specify the input sequences in a FASTA file.
    Fasta = alignment.FASTA

    #Specify the output Multifind file.
    Multifind = temp.Multifind

    #Specify the output structures in a group of CT files(optionally):
    #1. If OutCT option is inclued in the configuration file. There must be equal
    #   number of CT files as the number of sequences in the FASTA file.
    #2. If OutCT option is not included in the configuration file. The structures
    #   are not written out.
    OutCT = {1.ct;2.ct;3.ct;4.ct;5.ct;6.ct;7.ct;8.ct;}

    # Processors specifies the number of processors Multifind is run on.
    # Note that this flag only has an effect when Multifind-smp, the parallel version of Multifind, is run.
    # Its default value is 1.
    Processors = 1

### Notes:

Prebuilt executables are not provided for Multifind. Instructions for building can be found here.

### 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., Disney, M.D., Childs, J.L., Schroeder, S.J., Zuker, M. and Turner, D.H.
   "Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure."
   Proc. Natl. Acad. Sci. USA, 101:7287-7292. (2004).
3. Mathews, D.H., Sabina, J., Zuker, M. and Turner, D.H.
   "Expanded sequence dependence of thermodynamic parameters provides improved prediction of RNA secondary structure."
   J. Mol. Biol., 288:911-940. (1999).