RNAstructure Command Line Help |
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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:
Options that do not require added values:NONEOptions that require added values:NONEConfiguration 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 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:
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