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

tRNAscan-SE 1.21

The principles underlying the tRNAscan-SE program are described in:

Lowe, T.M. and Eddy, S.R. (1997)
tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence.
Nucleic Acids Res, 25, 955-964.

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).

Note (12/14/04): The Email Results function is fixed!

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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