This web server utilizes tRNAscan-SE 2.0

When using this web server, please cite one of the references.

Lowe, T.M. and Chan, P.P. (2016) tRNAscan-SE On-line: Search and Contextual Analysis of Transfer RNA Genes. Nucl. Acids Res. 44:W54-57.
Chan, P.P. and Lowe, T. M. (2019) tRNAscan-SE: Searching for tRNA Genes in Genomic Sequences. Methods Mol Biol. 1962:1-14.

When using the downloadable version of tRNAscan-SE 2.0 (below), please cite

Chan, P.P., Lin, B.Y., Mak, A.J., and Lowe, T.M. (2021) tRNAscan-SE 2.0: Improved Detection and Functional Classification of Transfer RNA Genes. Nucl. Acids Res. 49:9077–9096.


Source code: tRNAscan-SE-2.0.12.tar.gz
Change Log

tRNAscan-SE covariance model seed alignments (Stockholm format): tRNAscan-SE_CM_alignments.tar.gz

Example tRNA sequences

Search options
Sequence source
Search mode
Query sequence
Sequence name (optional):
(no spaces)
(Queries are limited to a total of less than 1 million nucleotides at any one time)

or submit a file:

Extended options
Disable pseudo gene checking
Show origin of first-pass hits
Show primary and secondary structure components to scores
Genetic Code for tRNA Isotype Prediction:
Score cutoff:

Default cut-off value should only be changed for execptional conditions