SEA-PHAGES | tRNAscan-SE

Link to this post \| posted yesterday, 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 yesterday, 17:11

Link to this post | posted yesterday, 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 yesterday, 17:11

Link to this post \| posted yesterday, 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 yesterday, 17:36 32Kb

Link to this post | posted yesterday, 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 yesterday, 17:36

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