Document Detail


PPfold 3.0: Fast RNA secondary structure prediction using phylogeny and auxiliary data.
MedLine Citation:
PMID:  22877864     Owner:  NLM     Status:  Publisher    
Abstract/OtherAbstract:
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.
Authors:
Zsuzsanna Sükösd; Bjarne Knudsen; Jørgen Kjems; Christianns Pedersen
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Publication Detail:
Type:  JOURNAL ARTICLE     Date:  2012-8-9
Journal Detail:
Title:  Bioinformatics (Oxford, England)     Volume:  -     ISSN:  1367-4811     ISO Abbreviation:  Bioinformatics     Publication Date:  2012 Aug 
Date Detail:
Created Date:  2012-8-10     Completed Date:  -     Revised Date:  -    
Medline Journal Info:
Nlm Unique ID:  9808944     Medline TA:  Bioinformatics     Country:  -    
Other Details:
Languages:  ENG     Pagination:  -     Citation Subset:  -    
Affiliation:
Interdisciplinary Nanoscience Center, Aarhus University, Ny Munkegade 120, Aarhus C, DK-8000, Denmark Department of Molecular Biology and Genetics, Aarhus University, C. F. Møllers Alle 3, Aarhus C, DK-8000, Denmark Bioinformatics Research Center, Aarhus University, C. F. Møllers Alle 8, Aarhus C, DK-8000, Denmark 4CLC bio, Finlandsgade 10-12, Aarhus N, DK-8200, Denmark Department of Computer Science, Aarhus University, Aabogade 34, Aarhus N, DK-8200, Denmark.
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