Background#R##N#The prediction of the structure of large RNAs remains a particular challenge in bioinformatics, due to the computational complexity and low levels of accuracy of state-of-the-art algorithms. The pfold model couples a stochastic context-free grammar to phylogenetic analysis for a high accuracy in predictions, but the time complexity of the algorithm and underflow errors have prevented its use for long alignments. Here we present PPfold, a multithreaded version of pfold, which is capable of predicting the structure of large RNA alignments accurately on practical timescales.
['Zsuzsanna Sükösd', 'Bjarne Knudsen', 'Morten Vaerum', 'Jørgen Kjems', 'Ebbe Sloth Andersen']
Multithreaded comparative RNA secondary structure prediction using stochastic context-free grammars