Comptes rendus de l’Acade'mie bulgare des Sciences, Vol 71, No9, pp.1215-1221

LoopRNA – Java Module for RNA Structure Annotation

Georgi Minkov, Valentina Toneva, Zdravka Ivanova, Vesselin Baev


LoopRNA is a Java module designed to add convenience and simplicity to the process of automatic RNA secondary structure annotation. By using concepts from Object-Oriented Programming and Mathematical Graph Theory, LoopRNA is able to present RNA secondary structure as a tree of discrete self-contained objects, arranged in a non-linear hierarchical “tree” structure. This produces data which is both easily human-readable and very simple to run otherwise complex automated computations on. While LoopRNA is not a standalone programme, integrating it into pre-existing Java software is trivial thanks to a simple and straightforward interface. Combined with existing premiRNA prediction software, LoopRNA can be applicable both to miRNA hairpin annotation and curation and to de novo prediction of miRNAs. LoopRNA is open source and is available under under the Creative Commons 4.0 licence (CC BY 4.0) at

Key words: RNA structure, annotation, object-oriented programming

DOI: 10.7546/CRABS.2018.09.08