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The tDRnamer web server is available at http://trna.ucsc.edu/tDRnamer/. Standalone software can be obtained from GitHub at https://github.com/UCSC-LoweLab/tDRnamer and a Docker image at https://hub.docker.com/r/ucsclowelab/tdrnamer. Example data can be downloaded from http://trna.ucsc.edu/tDRnamer/data/examples/. Prebuilt reference databases for model organisms are available at http://trna.ucsc.edu/tDRnamer/docs/refdb/. The complete set of tRFdb3 data reannotations by tDRnamer is available at http://trna.ucsc.edu/tDRnamer/data/tRFdb_reannotations/.
The source code of tDRnamer and the source code of its web server are available at https://github.com/UCSC-LoweLab/tDRnamer and https://github.com/UCSC-LoweLab/tDRnamer-web, respectively, both under the GNU General Public License v3.0.
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This work was supported by the National Human Genome Research Institute, National Institutes of Health (R01HG006753 to T.L.).
The authors declare no competing interests.
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 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). https://doi.org/10.1038/s41592-023-01813-2