Link to this post | posted 07 Dec, 2025 16:44
cdshaffer	Database 627 was released with 11 new phage. The whole phage starterator report for these phage have been added to the collection found here: https://wustl.box.com/v/Actino-phage New phage since the last update: BoogieWoogie CatBus DartGoblin DingDing DoubleChamp FleetyMac GroundGoblin HomeFry KikiBouba Noxious PowerRanger

Link to this post | posted 05 Dec, 2025 21:56

cdshaffer

Wow this is great work. Really good analysis on using alpha fold to discover the very likely localization and biological role for these proteins. I would say this goes way beyond what is expected for a typical annotation but really good work. Love the correlation of alphafold size predictions and physical observation in the EM. I only have one comment that really that has nothing to do with the role and function of these proteins but has more to do with nomenclature and a not that uncommon problem, so I think it is worth bringing up. If you look at the approved terms list you will see that Dit is mentioned twice. One approved term is just Dit and the other approved term is Dit/tail tip cage. Why is there two different terms and how would one know which one to pick? All this comes from the cryo EM work of Bxb1 done by Krista in the Hatfull lab. When she looked at gp32 in Bxb1 it is sitting right here where your protein is and she said that this Bxb1 protein is a fusion of two previously described proteins Dit and tail tip cage. Dit is the N terminal part of this Bxb1 protein and tail tip cage is the C term. So she named this with that double label. So I am seeing lots of good work that this protein is a Dit but I wonder, is it like Bxb1 and is it a fusion or is your phage the kind where the Dit and the tail tip cage are two separate polypeptides? I did not do an exhaustive search (sorry too much grading to do before grades are due), I did take Baconcheese 40 and do an HHPRED search to PDB, there was a very nice hit to the actual structure of that Bxb1 Dit/tail tip cage (9D93_Mf). Interestingly the alignment is not full length, only aa 75 to 275 of the 450 aa long BaconCheese protein aligned to aa 30 - 236 of the 685 aa Bxb1 Dit/tail tip cage. So the only part that is matching is the N term which is the Dit part. So my preliminary results would further support your annotation of just "Dit". If you want to dig deeper still, I would investigate what those unaligned amino acids at the C-term might be? They don't align to Bxb1 Dit/tail tip cage but they could align to some other tail tip cage or to something entirely different. Bottom line: I would certainly put my name on a paper that annotated this BaconCheese protein as Dit, but there might be something else going on here worthy of annotation at that C terminal end and a bit of further work might find it. On the other hand, an annotator always has to, at some point, say: "enough is enough, time to make the call" since there is not infinite time to investigate every protein. And so calling the "enough is enough" and annotating it Dit is totally fine in my book.

Link to this post | posted 29 Nov, 2025 02:44
cdshaffer	So sorry I missed this message. I usually come to this thread every week but we have had no new phage since middle of October. I have posted phage Phrampa in the O..R folder here: https://wustl.box.com/v/Actino-phage

Link to this post | posted 29 Nov, 2025 01:51

cdshaffer

Broken links to starterator reports are usually issues with starterator not PECAAN so you might want to cross post the message to the starterator topic as well. I just checked a dozen or so starterator links on PECAAN for the phage we are working on and they are all working so this may be a sporadic problem. Can you check again, if links are still broken, post the phage and gene (by location) that is specifically broken. Also as a reminder, if you have a phage that was sequenced in 2025 there should also be a whole phage report available for your phage. You can get to the report by going here: https://wustl.box.com/v/Actino-phage phage are sorted by phage name into one of the folders you find there. Edited 01 Dec, 2025 01:45

Link to this post | posted 18 Nov, 2025 23:50

cdshaffer

one more point to consider is that that A260/A280 ratio is the average expected when there is a very large number of different proteins. This makes sense when you purify your DNA from a whole cell. But phage have only a small number of proteins which can vary widely in the fraction of Trp, Tyr, and Phe. So the assumptions that underly that A260/A280 may not be valid for any particular phage. If you are worried about sequencing, I would not be. Those gels look pretty good and clearly there is nothing inhibiting restriction digests, so the DNA prep is probably just fine. Anyway there is my magic hand wavy argument for why I tend not to worry about those ratios when doing phage. But it does have a prediction which does allow one to propose an experiment, if you can get this phage sequenced. You could have the students look to see if there are a significantly different number of those critical amino acids in the structural genes for that one phage compared to some of the others which have given more typical ratios. Edited 18 Nov, 2025 23:53

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