| ## 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: Fu, Y., Xu, Z. Z., Lu, Z. J., Zhao, S., & Mathews, D. H. "Discovery of Novel ncRNA Sequences in Multiple Genome Alignments on the Basis of Conserved and Stable Secondary Structures." PLoS One. 10: e0130200. (2015). Reuter, J.S. and Mathews, D.H. "RNAstructure: software for RNA secondary structure prediction and analysis." BMC Bioinformatics, 11:129. (2010). 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). 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).