RNAiFold3.2 - Clotelab - Boston College

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COMPILING RNAiFold 3.2:

Requirements: - Software is developed in OR-Tools (https://github.com/google/or-tools), which is required for compiling RNAiFold. - A version of compiled Vienna Package libraries for Linux-amd64 is included. Download and compile the latest vienna libraries for your SO and copy libRNA.a file (from lib directory) into RNAiFold ViennaRNA directory. (This version is tested for ViennaRNA 2.1.9) - A version of compiled RNAstructure libraries for Linux-amd64 and OSX is included. Download (http://rna.urmc.rochester.edu/RNAstructure.html) Compile the latest RNAstructure libraries for your SO and libHybridRNA.so and libRNA.so to RNAiFold RNAstructure directory. (This version is tested for RNAstructure 5.7) Compilation step:

Download (https://github.com/google/or-tools/releases/tag/v7.3) and install OR-Tools 7.3 following the instructions in the installation guide included.
The expected default directory for OR-Tools installation is $(HOME)/OR-Tools-src/or-tools-7.3, if you install OR-Tools in a different directory change the value of ORTOOLS_DIR into Makefile
Assign the variable ORTOOLS_SRC in Makefile to the directory of your current OR-Tools installation
make

One single executable will be generated: RNAiFold

USAGE:

Only a target secondary structure is required for running RNAiFold, either as an input parameter or into the input file

Only a target secondary structure is required, which can be provided either as a parameter by command line flags or inside an input file. ./RNAiFold -RNAscdstr <SECONDARY_STRUCTURE> ./RNAiFold -InputFile <INPUT_FILE>

INPUT parameters: Design constraints can be provided as command line flags or inside the input file using the appropriate label preceeded by the "pound" symbol ("#") and writing the value in the next line. This are the valid labels/flags organized by sections.

Input file. -InputFile: (string) If provided, any parameters will be read from the given file. As explained parameters must be preceeded by the pound ('#') symbol Input File format: Input file must contain a valid secondary structure, all the other fields are optional, RNAiFold input file format is: > Fasta comment Target structure Sequence constraints # Parameter Parameter value

Target structure(s) and folding temperature(s) -RNAscdstr: (string) Input RNA secondary structure(s). To indicate multiple target structures they must be specified in the same line separated by the pipe '|' symbol. -temp: (string) Target folding temperature(s) in celsius. DEFAULT:37 To indicate multiple folding temperatures for the corresponding number of target structures write them in the same line separated by commas.

Number of solutions and search time limit: -TimeLimit: (int64) Search time limit in seconds. DEFAULT: 600 (10 minutes) -MAXsol: (int32) Input MAX solutions. DEFAULT:8

Sequence and structure compatibility: -RNAseqcon: (string) Input RNA sequence constraints. DEFAULT: -RNAcompstr: (string) Compatible RNA secondary structure. DEFAULT: -IncompBP: (string) List of incompatible base pairs. DEFAULT:

Thermodynamic parameters: -RNAlibrary: (string) RNA library for folding and computing energy values: Allowed models are: Vienna (ViennaRNA package) RNAstructure (Mathews' Lab). Default RNA library is ViennaRNA (Vienna). DEFAULT:Vienna -EnergyModel: (string) Energy model for ViennaRNa library. Allowed models are: 2004 (Turner '04), 1999 (Turner '99), 2007 (Andronescu '07) . Default energy model is Turner '04 (2004). DEFAULT:2004 -dangles: (int32) Dangling treatment. DEFAULT:2

Objective functions: -MFEstructure: (int32) Sequence MFE structure(s) must be the target structure(s). DEFAULT:1 -MinimizeEnsDef: (int32) Minimize ensemble defect for the target structure: print only sequences whose ensemble defect for the target structure is equal or lower than the previous one. DEFAULT:0 -MinimizeMFE: (int32) Minimize free energy of the MFE structure: print only sequences whose free energy when folded into their MFE structure is equal or lower than the previous one. DEFAULT:0

Local constraints: -HelixCstrs: (string) Helix local constraints. DEFAULT: -LocalCstrs: (string) Local constraints. DEFAULT:

Amino acid constraints: -AAseqcon: (string) List of amino acid sequence constraints. DEFAULT: -AAsimilCstr: (int32) Blosum similarity threshold (-4 to 4)(default 5 forces aminoacids to be equal to those specified) or allow similar amino acids based on a specific classification (6- Classification 1, 7-Classification 2 (see manual). DEFAULT:5 -AAstartPos: (string) List of starting positions for amino acid constraints. DEFAULT: -AAtarget: (string) List of target amino acid sequence for blosum similarity score maximization. DEFAULT:

Large neighborhood search: -LNS: (int32) Activate Large Neighborhood Search. DEFAULT:0 -LNSrestartTime: (int32) Maximum consecutive restarts in LNS without changes on fixed positions. DEFAULT:15 -LNStimeMultiplier: (int32) Multiplier for restart time in milliseconds (Time=length*multiplier). DEFAULT:0 -LNSunchangedRestarts: (int32) Maximum consecutive restarts in LNS without changes on fixed positions. DEFAULT:10 -MaxBlosumScore: (int32) Maximize blosum score of target sequences (default disabled). DEFAULT:0

Limit free energy of the structure: -MinMFE: (double) Minimum free energy allowed for the sequence folded into its minimum free energy structure. DEFAULT:1000 -MaxMFE: (double) Maximum free energy allowed for the sequence folded into its minimum free energy structure. DEFAULT:1000

Output parameters: -ShowMeasures: (int32) Show structural diversity measures. DEFAULT:1 -ShowHelices: (int32) Show helix identifiers for local constraints. This flag is only to visualize heclices, no search will be performed.

Nucleotide composition: -minAU: (int32) Minimum number of AU base pairs. DEFAULT:0 -maxAU: (int32) Maximum number of AU base pairs. DEFAULT:-1 -minGC: (int32) Minimum number of GC base pairs. DEFAULT:0 -maxGC: (int32) Maximum number of GC base pairs. DEFAULT:-1 -minGU: (int32) Minimum number of GU base pairs. DEFAULT:0 -maxGU: (int32) Maximum number of GU base pairs. DEFAULT:-1

 -minA: (string) List of minimum number of As in the full sequence (N) or in a specific range (N StartPos EndPos). DEFAULT:
 -maxA: (string) List of maximum number of As in the full sequence (N) or in a specific range (N StartPos EndPos). DEFAULT:
 -minC: (string) List of minimum number of Cs in the full sequence (N) or in a specific range (N StartPos EndPos). DEFAULT:
 -maxC: (string) List of maximum number of Cs in the full sequence (N) or in a specific range (N StartPos EndPos). DEFAULT:
 -minG: (string) List of minimum number of Gs in the full sequence (N) or in a specific range (N StartPos EndPos). DEFAULT:
 -maxG: (string) List of maximum number of Gs in the full sequence (N) or in a specific range (N StartPos EndPos). DEFAULT:
 -minU: (string) List of minimum number of Us in the full sequence (N) or in a specific range (N StartPos EndPos). DEFAULT:
 -maxU: (string) List of maximum number of Us in the full sequence (N) or in a specific range (N StartPos EndPos). DEFAULT:

 -consA: (string) List of maximum number of consecutive As in the full sequence (N) or in a specific range (N StartPos EndPos). DEFAULT:
 -consC: (string) List of maximum number of consecutive Cs in the full sequence (N) or in a specific range (N StartPos EndPos). DEFAULT:
 -consG: (string) List of maximum number of consecutive Gs in the full sequence (N) or in a specific range (N StartPos EndPos). DEFAULT:
 -consU: (string) List of maximum number of consecutive Us in the full sequence (N) or in a specific range (N StartPos EndPos). DEFAULT:

 -minGCcont: (double) Minimum GC content. DEFAULT:0
 -maxGCcont: (double) Maximum GC content. DEFAULT:100

Search parameters and heuristics: -RandomAssignment: (int32) Activate random value heuristic. DEFAULT:0 -BPthreshold: (int32) Probablility of selecting the next BP assignment in value heuristic. DEFAULT:85 -UPthreshold: (int32) Probablility of selecting the next UP assignment in value heuristic. DEFAULT:100 -VarHeuristic: (int32) Variable heuristic 1-Helices bottom to top 2-In to out . DEFAULT:2 -HelixHeuristic: (int32) Helix ordering heuristic for the search 1-Simple overlap 2-Base pair over

RNAiFold

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