TurboFold predicts the common structure for multiple sequences (two or more), using one of three folding modes. It has two distinct executables, a serial program called TurboFold and a parallelized program called TurboFold-smp for use in shared memory environments.

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:

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 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.
# <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.
################################################################

################################################################
# Input options
################################################################

# 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 = <mode specification>

# There are two separate ways to specify a group of input sequences:
# 1. Place sequence file names in brackets separated by semicolons.
#    Note that there cannot be any spaces whatsoever between the brackets.
#    The list must hold "SequenceNumber" sequences.
# 2. Each successive sequence "n" from 1 to SequenceNumber is specified as "Seq<n>."
#    Note that there cannot be any spaces in the file name.
InSeq = {seq1;seq2;seq3;}
Seq<n> = <seq file n>

# There are two separate ways to specify a group of output CT files:
# 1. Place CT file names in brackets separated by semicolons.
#    Note that there cannot be any spaces whatsoever between the brackets.
#    The list must hold "SequenceNumber" CT files.
# 2. Each successive CT file "n" from 1 to SequenceNumber is specified as "CT<n>."
#    Note that there cannot be any spaces in the file name.
OutCT = {ct1;ct2;ct3;}
CT<n> = <ct file n>

# SequenceNumber specifies the number of sequences given for calculation.
# This is only needed if both sequences and CT files are specified individually.
SequenceNumber = <number of sequences>

# Note that sequence file, CT file, and sequence number options must appear in one of two valid combinations, depending if files are
# specified singly or in a group.
#
# Singly:
# Mode = <mode>
# SequenceNumber = <n>
# Seq1 = <seq file 1>
# CT1 = <ct file n>
# ... repeat single entries of Seq and CT until <n> is reached
#
# Groups:
# Mode = <mode>
# InSeq = {seq1;seq2;seq3;}
# OutCT = {ct1;ct2;ct3;}

# Save<1> - Save<SequenceNumber> specifies the partiton function save file names to be outputted for each successive sequence "n"
# from 1 to SequenceNumber.
# Note that there cannot be any spaces in the file name.
# Save files are not required for any sequence.
Save<n> = <save file n>

# The output multiple sequence alignment filename can be specified. 
# Default is output.aln.
OutAln = filename


################################################################
# TurboFold options
################################################################

# Note that 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

# The number of columns of output multiple sequence alignment can be specified.
# Default is 60
ColumnNumber = 60

################################################################
# Maximum expected accuracy (MEA) mode options
################################################################

# Note that 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
################################################################

# Note that 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
################################################################

# Note that 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

################################################################
# Rsample mode options (using SHAPE data)
################################################################

# To apply SHAPE data on one or more sequences
UseRsample = 1
 
# Place shape file names in brackets separated by semicolons.
# The order is according to the list in InSeq.
# Note that there cannot be any spaces whatsoever between the brackets.
# For example, to apply SHAPE data on the first three sequences among five input sequences.
SHAPEFiles = {shape1;shape2;shape3;;;}

# Note that the following options only have an effect when ShapeFile and ShapeSeqIndex are specified. 
# If they are specified when TurboFold is in a different mode, they are ignored.

# To specify a seed number for stochastic sampling in Rsample mode.
Seed = 1

# Cparam and Offset specify the SHAPE constraints.
# 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

################################################################
# Traditional way to use SHAPE data mode options 
################################################################

# It is not required to specify any Rsample mode options.

# 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

                        

References:

1. Harmanci, A.O., Sharma, G., and Mathews, D.H.
   "TurboFold: Iterative Probabilistic Estimation of Secondary Structures for Multiple RNA Sequences."
   BMC Bioinformatics, 12:108. (2011).
2. Reuter, J.S. and Mathews, D.H.
   "RNAstructure: software for RNA secondary structure prediction and analysis."
   BMC Bioinformatics, 11:129. (2010).