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:

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. 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).
2. Reuter, J.S. and Mathews, D.H.
   "RNAstructure: software for RNA secondary structure prediction and analysis."
   BMC Bioinformatics, 11:129. (2010).
3. 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).
4. 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).