tRNAscan-SE Search Server
Lowe Lab
tRNAscan-SE Search Server
Search for tRNA genes in genomic sequence


tRNAscan-SE 1.21

This web server is described in
Schattner, P., Brooks, A.N., and Lowe, T.M. (2005) Nucleic Acids Res, 33: W686-689.
The principles underlying the tRNAscan-SE program are described in
Lowe, T.M. and Eddy, S.R. (1997) Nucleic Acids Res, 25: 955-964.
If you use this tool in your investigations, please cite one of these references.

Instructions for using the tRNAscan-SE server and interpreting the output can be found in the tRNAscan-SE README file.

If you would like to run tRNAscan-SE locally, you can get the UNIX source code (gzip'd tar file).

Analyzing tRNAs in a published genome?   See our own tRNAscan-SE analyses of completed genomes in the Genomic tRNA Database

Need some example tRNA sequences to try?
Search Mode: Source:


Standard formats (FASTA, GenBank, EMBL, GCG, IG)

Raw Sequence
Sequence name (optional): (no spaces)

Paste your query sequence(s) here:

(Queries are limited to a total of less than 5 million nucleotides at any one time)
or submit a file:
Show results in this browser.
Receive results by e-mail instead:

Output BED format

Extended Options:

Disable pseudo gene checking Show origin of first-pass hits
Display results in ACeDB format Show codons instead of tRNA anticodons
Show false positives from tRNAscan/EufindtRNA
Show primary and secondary structure components to Cove scores
Genetic Code for tRNA Isotype Prediction:

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

Cove score cutoff:

EufindtRNA search parameters:
Intermediate score cutoff:

Send comments/questions/problems using this search page or local installation of tRNAscan-SE to

Yeast tRNA-Phe image from Wikipedia

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