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

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PPfold 3.0: fast RNA secondary structure prediction using phylogeny and auxiliary data. / Sükösd, Zsuzsanna; Knudsen, Bjarne; Kjems, Jørgen; Pedersen, Christian Nørgaard Storm.

In: Bioinformatics, Vol. 28, No. 20, 09.11.2012, p. 2691-2692.

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Sükösd, Zsuzsanna ; Knudsen, Bjarne ; Kjems, Jørgen ; Pedersen, Christian Nørgaard Storm. / PPfold 3.0: fast RNA secondary structure prediction using phylogeny and auxiliary data. In: Bioinformatics. 2012 ; Vol. 28, No. 20. pp. 2691-2692.

Bibtex

@article{23c2485a7dfe4082b98d938bedc3966a,
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, zs@birc.au.dk.",
author = "Zsuzsanna S{\"u}k{\"o}sd and Bjarne Knudsen and J{\o}rgen Kjems and Pedersen, {Christian N{\o}rgaard Storm}",
year = "2012",
month = nov,
day = "9",
doi = "10.1093/bioinformatics/bts488",
language = "English",
volume = "28",
pages = "2691--2692",
journal = "Bioinformatics",
issn = "1367-4803",
publisher = "Oxford University Press",
number = "20",

}

RIS

TY - JOUR

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, zs@birc.au.dk.

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, zs@birc.au.dk.

U2 - 10.1093/bioinformatics/bts488

DO - 10.1093/bioinformatics/bts488

M3 - Journal article

C2 - 22877864

VL - 28

SP - 2691

EP - 2692

JO - Bioinformatics

JF - Bioinformatics

SN - 1367-4803

IS - 20

ER -