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

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

doi:10.1093/bioinformatics/bts488

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

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

Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaper › Journal article › Research › peer-review

45 Citations (Scopus)

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, [email protected].

Original language	English
Journal	Bioinformatics
Volume	28
Issue	20
Pages (from-to)	2691-2692
Number of pages	2
ISSN	1367-4803
DOIs	https://doi.org/10.1093/bioinformatics/bts488
Publication status	Published - 9 Nov 2012

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title = "PPfold 3.0: fast RNA secondary structure prediction using phylogeny and auxiliary data",

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 S{\"u}k{\"o}sd, [email protected].",

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T1 - PPfold 3.0: fast RNA secondary structure prediction using phylogeny and auxiliary data

AU - Sükösd, Zsuzsanna

AU - Knudsen, Bjarne

AU - Kjems, Jørgen

AU - Pedersen, Christian Nørgaard Storm

PY - 2012/11/9

Y1 - 2012/11/9

N2 - 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, [email protected].

AB - 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, [email protected].

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DO - 10.1093/bioinformatics/bts488

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EP - 2692

JO - Bioinformatics

JF - Bioinformatics

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ER -

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

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