title: PPfold 3.0: fast RNA secondary structure prediction using phylogeny and auxiliary data.
abstract: PPfold is a multi-threaded implementation of the Pfold algorithm for RNA secondary structure prediction. Here we present a new version of PPfold, which extends the evolutionary analysis with a flexible probabilistic model for incorporating auxiliary data, such as data from structure probing experiments. Our tests show that the accuracy of single-sequence secondary structure prediction using experimental data in PPfold 3.0 is comparable to RNAstructure. Furthermore, alignment structure prediction quality is improved even further by the addition of experimental data. PPfold 3.0 therefore has the potential of producing more accurate predictions than it was previously possible.
  
  
  METHODS
  PPfold 3.0 is available as a platform-independent Java application and can be downloaded from http://birc.au.dk/software/ppfold.
authors.affiliation: Interdisciplinary Nanoscience Center, Aarhus University, Aarhus N, Denmark. zs@birc.au.dk
authors.forename: Zsuzsanna
authors.initials: Z
authors.lastname: Sükösd
authors.forename: Bjarne
authors.initials: B
authors.lastname: Knudsen
authors.forename: Jørgen
authors.initials: J
authors.lastname: Kjems
authors.forename: Christian N S
authors.initials: CN
authors.lastname: Pedersen
mesh_terms: D000465:Algorithms; D015233:Models, Statistical; D009690:Nucleic Acid Conformation; D010802:Phylogeny; D012313:RNA / Q000737:chemistry*; D012984:Software
chemical_list: D012313:RNA