tRNAscan-SE 2.0 has advanced the state-of-the-art methodology in tRNA gene detection and functional prediction, captured by rich new content of the companion Genomic tRNA Database

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.

• tRNAscan-SE Main Site

• Module Name: trnascan-se (see the modules page for more information)
• Singlethreaded app
• Example files in /usr/local/apps/trnascan-se/TEST_DATA

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load trnascna-se
[+] Loading trnascan-se  2.0.0  on cn0166 

[user@cn3144 ~]$ cp /usr/local/apps/trnascan-se/TEST_DATA/ExampleSequences.fa .

[user@cn3144 ~]$ tRNAscan-SE ExampleSequences.fa

tRNAscan-SE v.2.0 (December 2017) - scan sequences for transfer RNAs
Copyright (C) 2017 Patricia Chan and Todd Lowe
                   University of California Santa Cruz
Freely distributed under the GNU General Public License (GPLv3)

------------------------------------------------------------
Sequence file(s) to search:        ExampleSequences.fa
Search Mode:                       Eukaryotic
Results written to:                Standard output
Output format:                     Tabular
Searching with:                    Infernal First Pass->Infernal
Isotype-specific model scan:       Yes
Covariance model:                  /usr/local/apps/trnascan-se/2.0.0/lib/tRNAscan-SE/models/TRNAinf-euk.cm
                                   /usr/local/apps/trnascan-se/2.0.0/lib/tRNAscan-SE/models/TRNAinf-euk-SeC.cm
Infernal first pass cutoff score:  10

Temporary directory:               /tmp
------------------------------------------------------------

Status: Phase I: Searching for tRNAs with HMM-enabled Infernal
Status: Phase II: Infernal verification of candidate tRNAs detected with first-pass scan
Sequence		tRNA	Bounds	tRNA	Anti	Intron Bounds	Inf	      
Name    	tRNA #	Begin	End	Type	Codon	Begin	End	Score	Note
--------	------	-----	------	----	-----	-----	----	------	------
MySeq1  	1	13 	85 	Thr	TGT	0	0	78.0	
MySeq2  	1	6  	79 	Arg	TCT	0	0	75.1	
MySeq3  	1	14 	114	Ser	CGA	51	69	71.8	
MySeq4  	1	6  	88 	Leu	AAG	0	0	65.0	
MySeq5  	1	3  	89 	SeC	TCA	0	0	146.9	
MySeq6  	1	7  	92 	Lys	CTT	0	0	72.1	

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. trnascan-se.sh). For example:

#!/bin/bash
set -e
module load trnascan-se
tRNAscan-SE ExampleSequences.fa

Submit this job using the Slurm sbatch command.

sbatch trnascan-se.sh

Create a swarmfile (e.g. trnascan-se.swarm). For example:

tRNAscan-SE ExampleSequences1.fa > out1.txt
tRNAscan-SE ExampleSequences2.fa > out2.txt
tRNAscan-SE ExampleSequences3.fa > out3.txt

Submit this job using the swarm command.

swarm -f trnascan-se.swarm --module trnascan-se