Reference : rPredictorDB: a predictive database of individual secondary structures of RNAs and th...
Scientific journals : Article
Engineering, computing & technology : Computer science
http://hdl.handle.net/10993/40651
rPredictorDB: a predictive database of individual secondary structures of RNAs and their formatted plots.
English
Jelinek, Jan [Charles University > Department of Software Engineering > > ; The Czech Academy of Sciences > Laboratory of Bioinformatics, Institute of Microbiology]
Hoksza, David mailto [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > > ; Charles University > Department of Software Engineering]
Hajic, Jan [Charles University > Department of Software Engineering]
Pesek, Jan [Charles University > Department of Software Engineering]
Drozen, Jan [Charles University > Department of Software Engineering]
Hladik, Tomas [Charles University > Department of Software Engineering]
Klimpera, Michal [Charles University > Department of Software Engineering]
Vohradsky, Jiri [The Czech Academy of Sciences > Laboratory of Bioinformatics, Institute of Microbiology]
Panek, Josef [The Czech Academy of Sciences > Laboratory of Bioinformatics, Institute of Microbiology]
2019
Database : the journal of biological databases and curation
2019
Yes
International
1758-0463
1758-0463
England
[en] 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.
Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group)
http://hdl.handle.net/10993/40651
10.1093/database/baz047
https://academic.oup.com/database/article/doi/10.1093/database/baz047/5479229

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