Skip to main content

Advertisement

Table 1 Main features of the interactive programs provided by the ViennaRNA Package 2.0

From: ViennaRNA Package 2.0

Program     Energy model variants    Data formats
  intramolecular bp intermolecular bp structure constraint canonical structures circular sequence dangling end model(s) centroid structure MEA structure suboptimal structures base pair probabilities/partition function input format(s) text output file(s) PostScript plot(s)
   single sequence analysis (global variant)     
RNAfold + - + + + 0,1,2,3 + + - + F,V - +
RNAsubopt + + + + + 0,1,2,3 NA NA B,E,Z - F,V - -
RNAcofold + + + + NA 0,1,2,3 - - - + F,V + +
RNAup + + + + - 0,2 - - - + V + -
RNAduplex - + - + - 0,1,2,3 - - E - V + -
RNA2Dfold* + - - - + 0,2 - + B - V - -
RNAPKplex* + - - + - 0,1,2,3 - - E - F,V - +
RNAplex* - + + - - 2 NA NA E - V,W + +
RNAsnoop* + + + + - 2 NA NA E - V,W + +
    single sequence analysis (local variant)     
RNALfold + - - + - 0,1,2,3 - - - - F,V - -
RNAplfold + - - + - 0,2 - - - - F,V + +
    comparative analysis (global variant)     
RNAalifold + - + + + 0,2 + + B + C,S - +
RNAaliduplex - + - + - 0,1,2,3 - - E - C,S + +
    comparative analysis (local variant)     
RNALalifold* + - - + - 0,1,2,3 - - - + C,S + +
     Misc. analysis/Utilities      
RNAeval + + NA NA + 0,1,2,3 NA NA NA NA F,V - -
RNAplot NA NA NA NA + NA NA NA NA NA F,V - +
RNAheat + - - + - 0,2 - - - - F,V - -
RNAinverse + - NA NA - 0,1,2,3 NA NA NA NA V - -
RNApaln + - - + - 0,1,2,3 NA NA NA + V + +
RNApdist + - - - - 0,1,2,3 NA NA NA + V + +
RNAdistance + - NA NA NA NA NA NA NA NA V + +
  1. The characters + and - show presence and absence of a certain feature, while NA indicates that the feature is not applicable in a given context. Abbreviations of input file formats are (C)lustal-format, (F)asta-format, (S)tockholm-format, and (V)iennaRNA-format. Support for prediction of suboptimal structures may be implemented as (B)oltzmann weighted sampling, exhaustive (E)numeration of all structures in a given energy band, and (Z)uker-style suboptimal structures. Programs marked by an asterisk (*) were not included in a previous release of the ViennaRNA Package.