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

tRNAscan-SE 1.21

Plea for letters of support: Our lab is planning major improvements and upgrades to the capabilites of tRNAscan-SE over the next 3-5 years. If you use this program and/or web service and find it helpful, please email a short letter of support to lowe@soe.ucsc.edu, describing briefly how tRNAscan-SE has helped advance your research, and voicing your support for future improvements (if you have specific feature requests, please include in your letter or email). tRNAscan-SE and this web server have been freely available for over ten years, and taking a few minutes to show your appreciation (and help us pursue future funding) is deeply appreciated. -TML

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


Search Mode: Source:

Format:

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

Other (FASTA, GenBank, EMBL, GCG, IG)

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:

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 lowe@soe.ucsc.edu
tRNA cartoon by
Tod Klingler
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