This page contains ADP implementations of grammars G1 to G6 from Dowell and Eddy's recent paper (R.D. Dowell and S.R. Eddy, Evaluation of several lightweight stochastic context-free grammars for RNA secondary structure prediction. BMC Bioinformatics, 5(71), 2004.):

Grammars:

 G1 :  S ->  aS | aS | Sa | SS | e              G4 :  S ->  aS | T | e
                                                       T ->  Ta | aS | TaS  

 G2 :  S      ->  aP^{a} | aS | Sa | SS | e    G5 :  S ->  aS | aS S | e
       P^{o} ->  aP^{a} | S            

 G3 :  S ->  aS | aL | Ra | LS                  G6 :   S ->  LS | L  
       L ->  aS | aL                                   L ->  aF | a  
       R ->  Ra | e                                     F ->  aF | LS  
Note: In contrast to other grammars for RNA folding, these stochastic grammars admit non-standard base pairing (with low probability).
To start, enter some input sequence, choose a grammar and a scoring scheme and press the "Go!" - Button.

Description of the scoring schemes:

For usage on your local machine:

Mechanical proof of non-ambiguity:

For the mechanical proof procedure you need an LR(k) parser generator. We recommend MSTA, which can be downloaded at http://cocom.sourceforge.net/. For our experiments we used version 0.995 (May 2002).
The file rna-grammars.tgz contains MSTA input files of the grammars G1 to G8 from Dowell and Eddy's paper.