Article (Scientific journals)
rPredictorDB: a predictive database of individual secondary structures of RNAs and their formatted plots.
Jelinek, Jan; Hoksza, David; Hajic, Jan et al.
2019In Database: The Journal of Biological Databases and Curation, 2019
Peer Reviewed verified by ORBi
 

Files


Full Text
baz047.pdf
Publisher postprint (8.45 MB)
Request a copy

All documents in ORBilu are protected by a user license.

Send to



Details



Abstract :
[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.
Research center :
- Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group)
Disciplines :
Computer science
Author, co-author :
Jelinek, Jan;  Charles University > Department of Software Engineering ; The Czech Academy of Sciences > Laboratory of Bioinformatics, Institute of Microbiology
Hoksza, David ;  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
External co-authors :
yes
Language :
English
Title :
rPredictorDB: a predictive database of individual secondary structures of RNAs and their formatted plots.
Publication date :
2019
Journal title :
Database: The Journal of Biological Databases and Curation
ISSN :
1758-0463
Publisher :
Oxford University Press, United Kingdom
Volume :
2019
Peer reviewed :
Peer Reviewed verified by ORBi
Available on ORBilu :
since 09 October 2019

Statistics


Number of views
67 (1 by Unilu)
Number of downloads
0 (0 by Unilu)

Scopus citations®
 
3
Scopus citations®
without self-citations
1
OpenCitations
 
3
WoS citations
 
3

Bibliography


Similar publications



Contact ORBilu