SEA-PHAGES | tRNAscan-SE

Link to this post \| posted 14 Apr, 2025 16:13
cdshaffer	As was discussed in the Friday CAT session tRNAscan has been down for a few days. The good news is that the program is also available for download and can be run on the command line. With that in mind I just processed all 750 odd phages that are marked as draft with tRNAscan-se. If your phage is missing post a follow-up message to this thread. You can get your results at the following link: http://phages.wustl.edu/trnascan/ Your results will be a zip archive with 3 files. These files are named starting with the Phage name and include "info", "struct", and "table" as part of the file name. The "info" file was created to confirm that the phage was analyzed and has the exact details on run parameters and version (you will need the version number if you intend to publish). For documentation here: tRNAscan-se was run with parameters "-X 0 -d -B -I -D -q" and the exact version was 2.0.12. The "struct" file contains the predicted structure of the tRNA as printed by tRNAscan-se. The "table" file contains the results in a table format very similar to the table results you get from the web page. If your genome has NO predicted tRNA's the "struct" and "table" files will be there but will be empty. Just be aware that the command line version does not produce those nice structure predictions like aragorn. The structure results look something like the text below and must be manually parsed. For this, the struct files are best viewed using a monospace font like consolas or courier (not available in forum posts): `eq: TCAGGTGcGGGGAAGATGGTAATCCGTTGGTTTTGGAAACCTAAGAcACCCGGTTCGATTCCGGGgCACCTGAC Str: >>>>>>>..>>>……….<<<.>.>>>…….<<<.<…..>>>>>…….<<<<<.<<<<<<<.` Edited 14 Apr, 2025 17:11

Link to this post | posted 14 Apr, 2025 16:13

As was discussed in the Friday CAT session tRNAscan has been down for a few days. The good news is that the program is also available for download and can be run on the command line. With that in mind I just processed all 750 odd phages that are marked as draft with tRNAscan-se. If your phage is missing post a follow-up message to this thread. You can get your results at the following link:

http://phages.wustl.edu/trnascan/

Your results will be a zip archive with 3 files. These files are named starting with the Phage name and include "info", "struct", and "table" as part of the file name.

The "info" file was created to confirm that the phage was analyzed and has the exact details on run parameters and version (you will need the version number if you intend to publish). For documentation here: tRNAscan-se was run with parameters "-X 0 -d -B -I -D -q" and the exact version was 2.0.12.

The "struct" file contains the predicted structure of the tRNA as printed by tRNAscan-se. The "table" file contains the results in a table format very similar to the table results you get from the web page.

If your genome has NO predicted tRNA's the "struct" and "table" files will be there but will be empty.

Just be aware that the command line version does not produce those nice structure predictions like aragorn. The structure results look something like the text below and must be manually parsed. For this, the struct files are best viewed using a monospace font like consolas or courier (not available in forum posts):


eq: TCAGGTGcGGGGAAGATGGTAATCCGTTGGTTTTGGAAACCTAAGAcACCCGGTTCGATTCCGGGgCACCTGAC
Str: >>>>>>>..>>>……….<<<.>.>>>…….<<<.<…..>>>>>…….<<<<<.<<<<<<<.

Edited 14 Apr, 2025 17:11

Link to this post \| posted 14 Apr, 2025 17:28
cdshaffer	As a follow-up. If you want to examine the predicted structures in 2D like aragorn you can use this site: https://rnacentral.org/r2dt Take any result from the tRNAscan struct file like this: `Seq: TCAGGTGcGGGGAAGATGGTAATCCGTTGGTTTTGGAAACCTAAGAcACCCGGTTCGATTCCGGGgCACCTGAC Str: >>>>>>>..>>>……….<<<.>.>>>…….<<<.<…..>>>>>…….<<<<<.<<<<<<<.` Get rid of the "seq:" and "Str:" replace all > with ( and all the < with ) and then add a header line starting with > and adding a description `>watermoore_tRNA4 TCAGGTGcGGGGAAGATGGTAATCCGTTGGTTTTGGAAACCTAAGAcACCCGGTTCGATTCCGGGgCACCTGAC (((((((..(((……….))).(.(((…….))).)…..(((((…….))))).))))))).` Paste that into the web page and hit run to get a nice colorful 2D rendering, see attached. Edited 14 Apr, 2025 17:36 32Kb

Link to this post | posted 14 Apr, 2025 17:28

cdshaffer

As a follow-up. If you want to examine the predicted structures in 2D like aragorn you can use
this site:

https://rnacentral.org/r2dt

Take any result from the tRNAscan struct file like this:

Seq: TCAGGTGcGGGGAAGATGGTAATCCGTTGGTTTTGGAAACCTAAGAcACCCGGTTCGATTCCGGGgCACCTGAC
Str: >>>>>>>..>>>……….<<<.>.>>>…….<<<.<…..>>>>>…….<<<<<.<<<<<<<.

Get rid of the "seq:" and "Str:" replace all > with ( and all the < with )
and then add a header line starting with > and adding a description

>watermoore_tRNA4
TCAGGTGcGGGGAAGATGGTAATCCGTTGGTTTTGGAAACCTAAGAcACCCGGTTCGATTCCGGGgCACCTGAC
(((((((..(((……….))).(.(((…….))).)…..(((((…….))))).))))))).

Paste that into the web page and hit run to get a nice colorful 2D rendering, see attached.

Edited 14 Apr, 2025 17:36

Link to this post \| posted 21 Apr, 2025 23:34
debbie	tRNA Scan SE may be back up, but it is still not showing the pictures. Please check the structure of the tRNAs if not available in tRNA Aragorn. Thanks, debbie

Link to this post \| posted 27 Oct, 2025 20:59
jrocheleau	tRNA Scan SE looks to be down again (since July 2025). What's the current protocol for detecting tRNAs? We are annotating BaconCheese, Mila11, SlySloth, and Kavo. Thanks, Jess

Link to this post \| posted yesterday, 20:24
cdshaffer	there are trivially easy to run at the command line. i have posted those 4 phage in the same server site as above. let me know if you have any trouble opening or reading the files as they are just text files not pretty HTML output, but they should do in a pinch. Anyone else need a tRNAscan feel free to post here and I will add those phage. The files have slightly different names but there is still the results list and the structures file. see here: http://phages.wustl.edu/trnascan P.S. click on "Last Modified" to sort by date, repeat if necessary to bring the most recent to the top of the list Edited yesterday, 20:27

Link to this post | posted yesterday, 20:24

cdshaffer

there are trivially easy to run at the command line. i have posted those 4 phage in the same server site as above. let me know if you have any trouble opening or reading the files as they are just text files not pretty HTML output, but they should do in a pinch.

Anyone else need a tRNAscan feel free to post here and I will add those phage.

The files have slightly different names but there is still the results list and the structures file. see here: http://phages.wustl.edu/trnascan

P.S. click on "Last Modified" to sort by date, repeat if necessary to bring the most recent to the top of the list

Edited yesterday, 20:27

Link to this post \| posted today, 19:12
cdshaffer	Just so everyone knows. Running tRNAscan on the desktop is trivially easy so if anyone else is working on a genome and needs results post them here or send me an email with the name of the phage and I will post the tRNAscan-se results to the server. Alternatively, if you have docker installed and are at least somewhat familiar with running docker on the command line I would be happy to share the protocol for using tRNAscan-se on the command line so you too could just run the tRNAscan-se analysis on your computer. This works on both intel and arm based machines and runs on both macOS and Windows.

Link to this post | posted today, 19:12

cdshaffer

Just so everyone knows. Running tRNAscan on the desktop is trivially easy so if anyone else is working on a genome and needs results post them here or send me an email with the name of the phage and I will post the tRNAscan-se results to the server.

Alternatively, if you have docker installed and are at least somewhat familiar with running docker on the command line I would be happy to share the protocol for using tRNAscan-se on the command line so you too could just run the tRNAscan-se analysis on your computer. This works on both intel and arm based machines and runs on both macOS and Windows.

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