PPfold 3.0: fast RNA secondary structure prediction using phylogeny and auxiliary data
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 experime...
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| Veröffentlicht in: | Bioinformatics (Oxford, England) England), 2012-10, Vol.28 (20), p.2691-2692 |
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| container_issue | 20 |
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| container_title | Bioinformatics (Oxford, England) |
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| creator | SÜKÖSD, Zsuzsanna KNUDSEN, Bjarne KJEMS, Jørgen PEDERSEN, Christian N. S |
| description | 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.
PPfold 3.0 is available as a platform-independent Java application and can be downloaded from http://birc.au.dk/software/ppfold. |
| doi_str_mv | 10.1093/bioinformatics/bts488 |
| format | Article |
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| ispartof | Bioinformatics (Oxford, England), 2012-10, Vol.28 (20), p.2691-2692 |
| issn | 1367-4803 1367-4811 |
| language | eng |
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| source | MEDLINE; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; Oxford Journals Open Access Collection; PubMed Central; Alma/SFX Local Collection |
| subjects | Algorithms Biological and medical sciences Fundamental and applied biological sciences. Psychology General aspects Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects) Models, Statistical Nucleic Acid Conformation Phylogeny RNA - chemistry Software |
| title | PPfold 3.0: fast RNA secondary structure prediction using phylogeny and auxiliary data |
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