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Jelínek J, Hoksza D, Hajič J, Pešek J, Drozen J, Hladík T, Klimpera M, Vohradský J, Pánek J. rPredictorDB: a predictive database of individual secondary structures of RNAs and their formatted plots. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2020; 2019:5479229. [PMID: 31032840 PMCID: PMC6482342 DOI: 10.1093/database/baz047] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 03/01/2019] [Accepted: 03/21/2019] [Indexed: 12/11/2022]
Abstract
Secondary data structure of RNA molecules provides insights into the identity and function of RNAs. With RNAs readily sequenced, the question of their structural characterization is increasingly important. However, RNA structure is difficult to acquire. Its experimental identification is extremely technically demanding, while computational prediction is not accurate enough, especially for large structures of long sequences. We address this difficult situation with rPredictorDB, a predictive database of RNA secondary structures that aims to form a middle ground between experimentally identified structures in PDB and predicted consensus secondary structures in Rfam. The database contains individual secondary structures predicted using a tool for template-based prediction of RNA secondary structure for the homologs of the RNA families with at least one homolog with experimentally solved structure. Experimentally identified structures are used as the structural templates and thus the prediction has higher reliability than de novo predictions in Rfam. The sequences are downloaded from public resources. So far rPredictorDB covers 7365 RNAs with their secondary structures. Plots of the secondary structures use the Traveler package for readable display of RNAs with long sequences and complex structures, such as ribosomal RNAs. The RNAs in the output of rPredictorDB are extensively annotated and can be viewed, browsed, searched and downloaded according to taxonomic, sequence and structure data. Additionally, structure of user-provided sequences can be predicted using the templates stored in rPredictorDB.
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Affiliation(s)
- Jan Jelínek
- Department of Software Engineering, Faculty of Mathematics and Physics, Charles University, Ke Karlovu, Praha.,Laboratory of Bioinformatics, Institute of Microbiology, The Czech Academy of Sciences, Videnska, Praha
| | - David Hoksza
- Department of Software Engineering, Faculty of Mathematics and Physics, Charles University, Ke Karlovu, Praha.,Luxembourg Centre for Systems Biomedicine, University of Luxembourg, avenue du Swing, Belvaux
| | - Jan Hajič
- Department of Software Engineering, Faculty of Mathematics and Physics, Charles University, Ke Karlovu, Praha
| | - Jan Pešek
- Department of Software Engineering, Faculty of Mathematics and Physics, Charles University, Ke Karlovu, Praha
| | - Jan Drozen
- Department of Software Engineering, Faculty of Mathematics and Physics, Charles University, Ke Karlovu, Praha
| | - Tomáš Hladík
- Department of Software Engineering, Faculty of Mathematics and Physics, Charles University, Ke Karlovu, Praha
| | - Michal Klimpera
- Department of Software Engineering, Faculty of Mathematics and Physics, Charles University, Ke Karlovu, Praha
| | - Jiří Vohradský
- Laboratory of Bioinformatics, Institute of Microbiology, The Czech Academy of Sciences, Videnska, Praha
| | - Josef Pánek
- Laboratory of Bioinformatics, Institute of Microbiology, The Czech Academy of Sciences, Videnska, Praha
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Jelínek J, Pánek J. cpPredictor: a web server for template-based prediction of RNA secondary structure. Bioinformatics 2019; 35:1231-1233. [PMID: 30169571 DOI: 10.1093/bioinformatics/bty753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 07/12/2018] [Accepted: 08/28/2018] [Indexed: 11/12/2022] Open
Abstract
SUMMARY We present the cpPredictor webserver that implements a novel template-based method for prediction of secondary structure of RNA. The method outperforms available prediction methods as it uses RNA structures of related molecules, either predicted or experimentally identified, as structural templates. The server aims at three major tasks: i) prediction of RNA secondary structures that are difficult to predict by available methods, ii) characterization of uncharacterized RNAs as compatible or incompatible with a chosen template structure and iii) an identification of the most relevant structure among different candidate structures of a single RNA ambiguously predicted by available methods. The web server is accompanied with a comprehensive documentation. AVAILABILITY AND IMPLEMENTATION The web server is freely available at http://cppredictor.elixir-czech.cz/. The source code of the cpPredictor algorithm is freely available from the webserver under the Apache License, Version 2.0.
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Affiliation(s)
- Jan Jelínek
- Laboratory of Bioinformatics, Institute of Microbiology, The Czech Academy of Sciences, Prague 1, Czech Republic
| | - Josef Pánek
- Laboratory of Bioinformatics, Institute of Microbiology, The Czech Academy of Sciences, Prague 1, Czech Republic
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