DAFS: simultaneous aligning and folding of RNA sequences by dual decomposition

Requirements

• Vienna RNA package (>= 1.8)
• (optional) GNU Linear Programming Kit (>=4.41) or Gurobi Optimizer (>=2.0) or ILOG CPLEX (>=12.0)

Install

export PKG_CONFIG_PATH=/path/to/viennarna/lib/pkgconfig:$PKG_CONFIG_PATH
mkdir build && cd build
cmake -DCMAKE_BUILD_TYPE=Release .. && cmake --build . 
cmake --install . # optional

To use "--ipknot" option for pseudoknotted common secondary structure prediction, build DAFS with an IP solver.

Usage

DAFS: dual decomposition for simultaneous aligning and folding RNA sequences.
Usage:
  dafs [OPTION...] FILE
	
  -h, --help             Print usage
  -w, --weight arg       Weight of the expected accuracy score for 
                     	  secondary structures (default: 4.0)
  -m, --max-iter T       The maximum number of iteration of the subgradient 
                     	  optimization (default: 600)
  -v, --verbose arg      The level of verbose outputs (default: 0)

  Aligning options:
  -a, --align-model arg     Alignment model for calcualating matching 
                        	  probablities (value=CONTRAlign, ProbCons) 
                        	  (default: ProbCons)
  -u, --align-th arg        Threshold for matching probabilities (default: 
                        	  0.01)

  Folding options:
  -s, --fold-model arg     Folding model for calculating base-pairing 
                       	  probablities (value=Boltzmann, Vienna, 
                       	  CONTRAfold) (default: Boltzmann)
  -t, --fold-th arg        Threshold for base-pairing probabilities 
                       	  (default: 0.2)
  -T, --fold-th1 arg       Threshold for base-pairing probabilities of the 
                       	  conclusive common secondary structures
  	  --ipknot             Set optimized parameters for IPknot decoding 
                       	  (--fold-decoder=IPknot -g4,8 -G2,4 --bp-update1)

Example

% dafs RF00005:0.fa
[ 0.0985233 [ 0.585795 [ 0.933469 M68929-1/151018-150946 X00360-1/1-73 ] [ 0.826623 X12857-1/421-494 [ 0.935672 J05395-1/2325-2252 M16863-1/21-94 ] ] ] [ 0.349897 [ 0.780743 J04815-1/3159-3231 [ 0.96716 J01390-1/6861-6932 M20972-1/1-72 ] ] [ 0.74278 K00228-1/1-82 AC009395-7/99012-98941 ] ] ]
>SS_cons
(((((((...(((..............))).......(((((..........)))))......(.((((.......))))).))))))).
> J01390-1/6861-6932
CAGGUUA-GAGCC-AGGU-GGU-UA--GGCG------UCUUGUUU--GG-GUCAAGA-AAUUGU-UAUGUUCGAAUCAUAA-UAACCUGA
> J05395-1/2325-2252
GGUUUCG-UGGUC-UAGUCGGUUAU--GGCA------UCUGCUUA--AC-ACGCAGA-ACGUCC-CCAGUUCGAUCCUGGG-CGAAAUCG
> K00228-1/1-82
GGUUGUUUG-GCCGA-GC-GGU-CUAAGGCGCCUGAUUCAAGCUCAGGU-AUCGUAA--GAUGCAAGAGUUCGAAUCUCUU-AGCAACCA
> AC009395-7/99012-98941
GGCUCAA-U----------GGU-CUAG-GGGUAUGAUUCUCGCUUUGGG-UGCGAGA--GGUCC-CGGGUUCAAAUCCCGG-UUGAGCCC
> J04815-1/3159-3231
AGAGCUU-GCUCC-CAAA-GCU-UG--GGUG------UCUAGCUG--AU-AAUUAGA-CUAUCA-AGGGUUAAAUUCCCUUCAAGCUCUA
> M20972-1/1-72
AGGGCUA-UAGCU-CAGC-GGU-AG--AGCG------CCUCGUUU--AC-ACCGAGA-AUGUCU-ACGGUUCAAAUCCGUA-UAGCCCUA
> M68929-1/151018-150946
CGCGGGA-UAGAG-UAAUUGGU-AA--CUCG------UCAGGCUC--AU-AAUCUGA-AUGUUG-UGGGUUCGAAUCCGAC-UCCCGCCA
> X00360-1/1-73
CCGACCU-UAGCU-CAGUUGGU-AG--AGCG------GAGGACUG---UAGAUCCUU-AGGUCA-CUGGUUCGAAUCCGGU-AGGUCGGA
> X12857-1/421-494
GCGGAUG-UAGCC-AAGUGGAUCAA--GGCA------GUGGAUUG--UG-AAUCCACCAUG-CG-CGGGUUCAAUUCCCGU-CAUUCGCC
> M16863-1/21-94
GGGCUCG-UAGCU-CAGAGGAUUAG--AGCA------CGCGGCUA--CG-AACCACG-GUGUCG-GGGGUUCGAAUCCCUC-CUCGCCCA

References

• Sato, K., Kato, Y., Akutsu, T., Asai, K., Sakakibara, Y.: DAFS: simultaneous aligning and folding RNA sequences via dual decomposition. Bioinformatics, 28(24):3218-3224, 2012.