PPfold 3.0: fast RNA secondary structure prediction using phylogeny and auxiliary data

Zsuzsanna Sükösd, Bjarne Knudsen, Jørgen Kjems, Christian Nørgaard Storm Pedersen

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Abstract

Summary PPfold is a multithreaded 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.Availability and Implementation PPfold 3.0 is available as a platform-independent Java application, and can be downloaded from http://birc.au.dk/software/ppfold. CONTACT: Zsuzsanna Sükösd, zs@birc.au.dk.
OriginalsprogEngelsk
TidsskriftBioinformatics
Vol/bind28
Nummer20
Sider (fra-til)2691-2692
Antal sider2
ISSN1367-4803
DOI
StatusUdgivet - 9 nov. 2012

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