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tRNAScan-SE Down-ish?

| posted 24 Sep, 2020 10:22
Hello,

Several students have reported to me that they are not getting results from tRNAScan-SE over the last week. So I just tried it, and let it run all night and had the same experience. It just stalled while working on a cluster BE, which has lots, and lots of tRNAs.

Does anyone know something about tRNAScan-SE?

Thanks,

Steve
| posted 24 Sep, 2020 11:46
Hi Steve,
This is likely due to the wild fires in California. It appears that folks can be back on campus, but if the Lowe lab can't get to their servers, tRNA-ScanSE is in jeopardy.
debbie
| posted 24 Sep, 2020 12:02
Thank you. I am going to advise they use Aragorn for now and revisit with tRNAScan-SE later in the semester, unless you suggest otherwise.

Steve
| posted 24 Sep, 2020 20:02
For those of you that have the SEAVM with pdm utils installed that came out in June 2020, it has version 2.0.5 of tRNA-scan already installed. It is the command line version, not the web page, but it is pretty straightforward to run.

First copy the genome fasta file into the VM and put the file on the Desktop. Open a terminal and change the working directory to the Desktop with this command:

cd Desktop

Now use the following command (I tried to use the parameter settings that would mimic the settings recommended on the web interface). You will need to replace the items bounded by the <> with your specific values:

tRNAscan-SE -B -I –max -D -o <name of file with results> <name of fasta file>

Here is an example of the command I used recently on phage Jada where the fasta genome file is called Jada.fasta, and I wanted the results file to be called Jada.tRNAscan.txt.

tRNAscan-SE -B -I –max -D -o Jada.tRNAscan.txt Jada.fasta

the results will be a text file that you can copy back to your computer, it can be opened by textedit on a Mac or Wordpad on Windows. Here are the first few lines of the output for phage Jada:

Sequence		tRNA  	Bounds	tRNA	Anti	Intron Bounds	Inf
Name    	tRNA #	Begin 	End   	Type	Codon	Begin	End	Score	N
——–	——	—– 	——	—-	—–	—–	—-	——	—
Jada    	1	65495 	65565 	Pro	TGG	0	0	50.1
Jada    	2	65734 	65808 	Pro	TGG	0	0	72.6
Jada    	3	66800 	66873 	Gln	CTG	0	0	54.6
Jada    	4	66926 	66996 	Trp	CCA	0	0	26.0
Jada    	5	67273 	67347 	Ile	GAT	0	0	68.1
Jada    	6	67752 	67835 	Ser	TGA	0	0	42.0	
| posted 24 Sep, 2020 20:07
Thank you, Chris. I will give that a try!

Steve
| posted 25 Sep, 2020 00:24
Chris,

Excellent. And thank you for the very clear directions with sample. Worked perfectly.

Steve
 
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