RNAstructure Command Line Help |
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TurboFold predicts the common structure for two or more RNA sequences. It does this by generating pairwise alignments between sequences using a hidden markov model (HMM), which supplies extrinsic information to one of three selectable folding modes. The alignments and folding output are iteratively used to improve each other. USAGE 1: TurboFold <configuration file>USAGE 2: TurboFold-smp <configuration file>Required parameters:
Options that do not require added values:
Options which require added values:NONENotes:
Configuration file format:The following is a description of valid options allowed in the configuration file. # IMPORTANT CONFIG FILE FORMAT NOTES: # # Option lines may be specified by the option name followed by an equals sign # and the option's desired value. Option names are not case sensitive. # 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. # Mode specifies the resolving algorithm TurboFold uses after its initial fold. # A valid mode is required for TurboFold to run properly. # Valid modes can be one of three options: # 1. MEA (Maximum expected accuracy) # 2. ProbKnot (For pseudoknotted sequences) # 3. Threshold (Finding most probable pairs) # Modes should be specified as text strings: MEA, ProbKnot, or Threshold. # The default mode is MEA. Mode = MEA|ProbKnot|Threshold # SequenceNumber specifies the number of sequences given for calculation. # This is only needed if both sequences and CT files are specified # individually (see below). SequenceNumber = <number of sequences> #### Listing Input Sequences #### # There are two formats in which input sequence files can be specified -- either # grouped or individually. # # 1. Grouped: Place sequence file names in brackets separated by semicolons. # Filenames may contain spaces, but no extra space is allowed before or after # semicolons or braces. InSeq = {path/to/input1.seq;path/to/input2.seq;path/to/input3.seq;} # # 2. Individually: Each successive sequence is specified as "Seq<N>" where <N> goes # from 1 to SequenceNumber. # The file names cannot contain spaces in this format. SequenceNumber = 3 Seq1 = path/to/input1.seq Seq2 = path/to/input2.seq Seq3 = path/to/input3.seq #### Listing Output CT files #### # There are two formats in which output CT files can be specified -- either # grouped or individually. # # 1. Grouped: Place CT file names in brackets separated by semicolons. # Filenames may contain spaces, but no extra space is allowed before or after # semicolons or braces. OutCT = {path/to/output1.ct;path/to/output2.ct;path/to/output3.ct;} # # 2. Individually: Each successive sequence is specified as "CT<N>" where <N> goes # from 1 to SequenceNumber. # The file names cannot contain spaces in this format. CT1 = path/to/output1.ct CT2 = path/to/output2.ct CT3 = path/to/output3.ct # Partiton function save file (PFS) names can be specified for each sequence # if this type of output is desired. These can be listed individually or grouped. # Save files are not required. # Individually: # Save<N> (where <N> goes from 1 to SequenceNumber). # There cannot be any spaces in the file names. Save<N> = <save file N> # or Grouped: SaveFiles = {path/to/file1.pfs;path/to/file2.pfs;path/to/file3.pfs;} # The output multiple sequence alignment filename can be specified. # Default is output.aln. OutAln = <filename> ################################################################ # TurboFold options ################################################################ # TurboFold options affect output regardless of the mode specified. # Gamma specifies the TurboFold gamma value. # This should not be confused with MeaGamma (below). # Its default value is 0.3. Gamma = 0.3 # Iterations specifies the number of iterations TurboFold goes through. # This should not be confused with PkIterations (below). # Its default value is 3. Iterations = 3 # MaximumPairingDistance specified the maximum distance between nucleotides that can pair. # i.e. for nucleotide i to pair with j, [i - j| < MaximumPairingDistance. # This applies to each sequence. # Its default is no limit, which is indicated by a value of zero. MaximumPairingDistance = 0 # Temperature specifies the temperature at which TurboFold is run, in Kelvin. # Its default value is 310.15 K, which is 37 degrees C. Temperature = 310.15 # Processors specifies the number of processors TurboFold is run on. # Note that this flag only has an effect when TurboFold-smp, the parallel version # of TurboFold, is run. # Its default value is 1. Processors = 1 # The format of output multiple sequence alignment can be choosen from Fasta or Clustal. # Default is Clustal. AlnFormat = Fasta|Clustal # The number of columns of output multiple sequence alignment can be specified. # Default is 60 ColumnNumber = 60 ################################################################ # Maximum expected accuracy (MEA) mode options ################################################################ # The following options only have an effect when MEA mode is specified. # If they are specified when TurboFold is in a different mode, they are ignored. # MaxPercent specifies the maximum percent energy difference. # Its default value is 50 (percent). MaxPercent = 50 # MaxStructures specifies the maximum number of structures to calculate. # Its default value is 1000 structures. MaxStructures = 1000 # MeaGamma specifies the MEA mode gamma value. # This should not be confused with Gamma (above). # Its default value is 1.0. MeaGamma = 1.0 # Window specifies the window size. # Its default value is 5 nucleotides. Window = 5 ################################################################ # Pseudoknot (ProbKnot) mode options ################################################################ # The following options only have an effect when ProbKnot mode is specified. # If they are specified when TurboFold is in a different mode, they are ignored. # MinHelixLength is the minimum helix length allowed during folding. # Its default value is 3 nucleotides. MinHelixLength = 3 # Iterations specifies the number of iterations ProbKnot goes through. # This should not be confused with Iterations (above). # Its default value is 1. PkIterations = 1 ################################################################ # Probable Pairs (Threshold) mode options ################################################################ # The following options only have an effect when Threshold mode is specified. # If they are specified when TurboFold is in a different mode, they are ignored. # Threshold specifies the probability threshold at which pairs are included in a structure. # If a threshold is explicitly specified, it should be expressed as a number >= 0.5 and <= 1.0. # Its default value is 0. # This signifies that structures should be generated at the following thresholds: # >= 0.99, >= 0.97, >= 0.95, >= 0.90, >= 0.80, >= 0.70, >= 0.60, >= 0.50 Threshold = 0 ################################################################ # Using SHAPE data ################################################################ # To apply SHAPE data on one or more sequences, use the SHAPEFiles option and $ place shape file names in brackets separated by semicolons. # The order of the files should correspond to list of input sequences. # Note that there cannot be any spaces whatsoever between the brackets or semicolons. # The shape file name can be left blank for sequences that lack shape data. # For example, the following line applies SHAPE data to sequences 1, 2, and 4, but # not to sequences 3 and 5. (Note the empty slots in the 3rd and 5th positions). SHAPEFiles = {file1.shape;file2.shape;;file4.shape;;} # SHAPE files can also be specified individually, which is often more # straightforward when only a few input sequences have SHAPE data: SHAPE1 = file1.shape SHAPE4 = file4.shape # SHAPEintercept specifies the SHAPE intercept used by TurboFold. # Note that if specified, this value is only used if one or more SHAPE files is also specified. # Its default value is -0.6 kcal/mol. SHAPEintercept = -0.6 # SHAPEslope specifies the SHAPE slope used by TurboFold. # Note that if specified, this value is only used if one or more SHAPE files is also specified. # Its default value is 1.8 kcal/mol. SHAPEslope = 1.8 ##### Using Rsample Mode for SHAPE data ##### # Rsample is a more accurate method of using SHAPE data, which uses stochastic # sampling to match SHAPE values to structural motifs. # Rsample mode can be enabled with the following option. # (If Rsample is not enabled, SHAPE data are used in legacy mode.) UseRsample = 1 # The following options only have an effect when Rsample is enabled. # Specify a seed number for stochastic sampling in Rsample mode. Seed = 1 # Cparam and Offset specify the SHAPE constraints in Rsample mode. # Cparam is used to establish the relationship between free energy and reactivities. # Offset is used to account for the fact that normalized reactivities can be less than zero. # The default values for Cparam is 0.5; for Offset is 1.1. Cparam = 0.5 Offset = 1.1 # NumSamples specify the number of samples for stochastic sampling in Rsample mode. # The default value is 10000. NumSamples = 10000 References:
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