Link to this post | posted 30 Oct, 2025 20:06

cdshaffer

I can answer the easy question. This board has a set of automatic emoji's (you can see then across the bottom of the text entry window) and a couple of them end in ) so you typed the evalue which ended in 8 and then the end paren. This is automatically converted to the emoji with the dark glasses. The best way to guard against these it to hit the green check mark. This will create a representation of how your post will look when posted and you can look for accidental emojis. The easiest way I know to avoid this is the add a space before the parentheses.

Link to this post | posted 29 Oct, 2025 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 28 Oct, 2025 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 28 Oct, 2025 20:27

Link to this post | posted 18 Oct, 2025 01:38
cdshaffer	Database 619 was released with 1 new phage. The whole phage starterator report for this phage have been added to the collection found here: https://wustl.box.com/v/Actino-phage New phage in 619: Grayscar

Link to this post | posted 03 Oct, 2025 17:24

cdshaffer

This raises an interesting issue about starterator numbering and while not directly related to the question at hand above (start 1 vs start 10) it is an important point in interpretation of starterator results and why Deb talks about starts 9, 10 & 11. I will give a super simple example of why it is recommended that if there are two (or more) starts that look very close in the graphical track you can consider them "the same". Here are two made up sequences that demonstrates how small sequence changes can lead clustal to artificially create different start numbers. I will use a tiny sequence right around a start codon with the smallest possible change of the insertion of a single base. Here are the two sequences: CCCATGCCC & CCCAATGCCC When clustal aligns these two the result will align like this: CCCA-TGCCC |||| ||||| CCCAATGCCC When starterator looks at this alignment the two strands do not have identical locations (the top strand has an ATG starting at base 4 of the alignment and the bottom strand has an ATG starting at base 5 of the alignment). So these two sequences will get different start numbers. But these two sequences really do have the same start, as Deb says, this is an issue with how clustal does the alignment as sequences diverge. Bottom line: don't over interpret different start numbers to mean "absolutely must be different starts if they are different numbers", instead look at the tracks at the top of the report, if the starts are tightly clustered you can assume that there are minor base differences but the starts all very likely trace back to a single start in the common ancestor and can thus be considered "the same start". Edited 03 Oct, 2025 17:37

Link to this post | posted 26 Sep, 2025 03:01
cdshaffer	Database 615 was released with 8 new phage. The whole phage starterator reports for these phage have been added to the collection found here: https://wustl.box.com/v/Actino-phage New phage in 613: ChutneyChips HippoHollow Impisi Medindi NovoPizza PaintedDog Saskia ZamZam

Link to this post | posted 14 Sep, 2025 20:09
cdshaffer	Database 613 was released with 7 new phage. The whole phage starterator reports for these phage have been added to the collection found here: https://wustl.box.com/v/Actino-phage New phage in 613: CarefulCloud HorseRider IUFootball Jalloh PhirstandPhine Rooter TailX7 Edited 14 Sep, 2025 20:09

Link to this post | posted 11 Sep, 2025 16:19
cdshaffer	Database 612 was released with 2 new phage. The whole starterator reports for these phage have been added to the collection found here: https://wustl.box.com/v/Actino-phage New phage in 612: Lunareta Montpel

Link to this post | posted 30 Aug, 2025 02:41
cdshaffer	Database 611 was released with 4 new phage. The whole starterator reports for these phage have been added to the collection found here: https://wustl.box.com/v/Actino-phage New phage in 611: Dialga, Flashwig, Grumio, WST1

Link to this post | posted 25 Aug, 2025 18:29
cdshaffer	Database 610 was released with 2 new phage. The whole starterator reports for these phage have been added to the collection found here: https://wustl.box.com/v/Actino-phage New phage in 610: ArizonaGT, Schlegelian