bpRNA: large-scale automated annotation and analysis of RNA secondary structure

@article{Danaee2018bpRNALA,
  title={bpRNA: large-scale automated annotation and analysis of RNA secondary structure},
  author={Padideh Danaee and Mason Rouches and Michelle Wiley and Dezhong Deng and Liang Huang and David A. Hendrix},
  journal={Nucleic Acids Research},
  year={2018},
  volume={46},
  pages={5381 - 5394}
}
While RNA secondary structure prediction from sequence data has made remarkable progress, there is a need for improved strategies for annotating the features of RNA secondary structures. Here we present bpRNA, a novel annotation tool capable of parsing RNA structures, including complex pseudoknot-containing RNAs, to yield an objective, precise, compact, unambiguous, easily-interpretable description of all loops, stems, and pseudoknots, along with the positions, sequence, and flanking base pairs… 

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