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A standardized ontology for naming tRNA-derived RNAs based on molecular origin

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Fig. 1: Standardized naming for tRNA-derived RNAs (tDRs) illustrated by seven tDRs potentially derived from up to eight human tRNAPro transcripts.

Data availability

The tDRnamer web server is available at Standalone software can be obtained from GitHub at and a Docker image at Example data can be downloaded from Prebuilt reference databases for model organisms are available at The complete set of tRFdb3 data reannotations by tDRnamer is available at

Code availability

The source code of tDRnamer and the source code of its web server are available at and, respectively, both under the GNU General Public License v3.0.


  1. Cozen, A. E. et al. Nat. Methods 12, 879–884 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Shi, J. et al. Nat. Cell Biol. 23, 424–436 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Kumar, P., Mudunuri, S. B., Anaya, J. & Dutta, A. Nucleic Acids Res. 43, D141–D145 (2015).

    Article  CAS  PubMed  Google Scholar 

  4. Gebetsberger, J. & Polacek, N. RNA Biol. 10, 1798–1806 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Polacek, N. & Ivanov, P. RNA Biol. 17, 1057–1059 (2020).

    Article  PubMed  PubMed Central  Google Scholar 

  6. Kim, H. K., Yeom, J. H. & Kay, M. A. Mol. Ther. 28, 2340–2357 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Magee, R. & Rigoutsos, I. Nucleic Acids Res. 48, 9433–9448 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Pliatsika, V. et al. Nucleic Acids Res. 46 (D1), D152–D159 (2018).

  9. Chan, P. P. & Lowe, T. M. Nucleic Acids Res. 44 (D1), D184–D189 (2016).

  10. Steinberg, S., Misch, A. & Sprinzl, M. Nucleic Acids Res. 21, 3011–3015 (1993).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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This work was supported by the National Human Genome Research Institute, National Institutes of Health (R01HG006753 to T.L.).

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Authors and Affiliations



A.H. and P.C. designed and developed tDRnamer standalone software. P.C. designed and developed the tDRnamer web server. P.C. and T.L. wrote the manuscript. All authors contributed to the design of tDR naming convention and the feature requirements of tDRnamer.

Corresponding author

Correspondence to Todd M. Lowe.

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Competing interests

The authors declare no competing interests.

Peer review

Peer review information

Nature Methods thanks Hani Goodarzi and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

Supplementary information

Supplementary Information

Supplementary Figs. 1–3, Tables 1–4 and Methods

Supplementary Data 1

Reannotation of human tRNA-derived RNAs in tRFdb using tDRnamer

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Holmes, A.D., Chan, P.P., Chen, Q. et al. A standardized ontology for naming tRNA-derived RNAs based on molecular origin. Nat Methods (2023).

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