Using the tRNAscan-SE Web Server

The tRNAscan-SE server is accessed via the Lowe Lab Webserver Interface at  http://lowelab.cse.ucsc.edu/tRNAscan-SE/.

User Interface

The tRNAscan-SE interface consists of three major components:
* Search mode selection
* Query sequence selection
* Configuration of search-mode and options for displaying results

The search mode determines which probabilistic model to use in searches – each model is based on tRNA training data from selected species or phylogenetic groups (i.e., mammals, yeasts, archaea). If no explicit model for the species of interest is available in the user interface, specifying either a general model or a model from a related species generally yields good results. Different search modes can offer varying speed and sensitivity.  For tRNAscan-SE, the standard search modes are fast and very sensitive in most instances.  However, for short sequences that contain extremely atypical tRNAs, the “Cove only” mode offers slightly improved sensitivity (this is the default search mode for organellar sequence searches).

Query sequence selection is used to specify the sequences to be searched for tRNAs. Raw or formatted sequence data can be pasted directly into the query sequence box or can be uploaded from a local file. Links to sample query sequence data are also available for demonstration purposes.

The server also has a set of program-specific search and output-display options such as the tRNA isotype code. In addition, the server has an adjustable cutoff score enabling tradeoffs between scan sensitivity and specificity. In most cases, the default parameter choices will be satisfactory and should be selected – especially by new users. However, more experienced users are able to exert some control over the program’s results by manipulating these parameters.

Output format

The default output for tRNAscan-SE includes overall statistics for the various component programs (trnascan(14), eufindtrna(15) and cove(16)) as well as summary data for the entire search. The summary data includes counts of the total number of tRNAs found, the number of tRNA pseudogenes found, number of tRNAs with introns and which anticodons were detected. Finally, the output shows the predicted secondary structure for each identified sequence.  With an additional click on the “View tRNA” button to the right of each tRNA, a two-dimensional representation of the tRNA structure can be displayed, producing the familiar tRNA clover-leaf structure.  The output also displays the overall length of the sequence, the location of the anticodon and the overall tRNAscan-SE score. tRNAscan-SE scores for known tRNA sequences for various species are included on the website to facilitate evaluation of the significance of the score.


Sample (abbreviated) tRNAscan-SE Output

Sequence		tRNA	Bounds	tRNA	Anti	Intron Bounds	Cove
Name			tRNA #	Begin	End	Type	Codon  Begin	End	Score
--------		------	----	------	----	-----  -----	----	------

Your-seq		1	1	73	Ala	AGC    0	0	74.48


Summary
--------
Overall scan speed: 730.0 bp/sec

tRNAs decoding Standard 20 AA:              1
Selenocysteine tRNAs (TCA):                 0
Possible suppressor tRNAs (CTA,TTA):        0
tRNAs with undetermined/unknown isotypes:   0
Predicted pseudogenes:                      0
                                            -------
Total tRNAs:                                1

tRNAs with introns:			    0


Isotype / Anticodon Counts:

Ala   : 1   AGC: 1       GGC:         CGC:         TGC:       

------------------------------------------------------------------------

Predicted tRNA Secondary Structures:

Your-seq.trna1 (1-73)	       Length: 73 bp
Type: Ala      Anticodon: AGC at 34-36 (34-36)	Score: 74.48
         *    |    *    |    *    |    *    |    *    |    *    |    *    |  
Seq: GGGCGTGTGGCGTAGTCGGTAGCGCGCTCCCTTAGCATGGGAGAGGtCTCCGGTTCGATTCCGGACTCGTCCA
Str: >>>>>.>..>>>>........<<<<.>>>>>.......<<<<<.....>>>>>.......<<<<<<.<<<<<.

Further information

The tRNAscan-SE algorithm is 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 Research, 25, 955-964.

Additional information can be found in the User Manual for command-line UNIX version of the program.