Link to this post | posted 06 May, 2025 17:36
debbie	Aurturo, Please use PineapplePizza as your prototype as to what to call each tail type in your pododvirus. I used P68 and phi29 as the prototypes to call that one. For genes 17 and 18 of Smelly (phamerator_draft), you can call both as minor tail proteins. Once you do that, If you have any questions, continue on the forum post. Thanks, debbie

Link to this post | posted 05 May, 2025 15:19
debbie	Nikki, The data is coming fast and furious. For now, I would call these Hypothetical Proteins. but soon, we may have a better understanding. Best, debbie

Link to this post | posted 01 May, 2025 23:28
debbie	Hi all, When annotating a Cluster O paper, please refer to this paper for help "Comparative Genomics of Cluster O Mycobacteriophages" https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0118725

Link to this post | posted 01 May, 2025 23:19
debbie	Iain, Did you have a working DNA master? If not use this forum post to install. https://seaphages.org/forums/topic/5577/ If you did have a working copy, it has not been updated since Oct 24, 2021. The server where it sat is no more. So there is no need to update and you can't because the server is not available any more. We are working on it. The link above does work. debbie

Link to this post | posted 01 May, 2025 16:40
debbie	Arturo, Sure that will work. It would also be appropriate to call it a "endolysin, protease M15 domain". (I like this one better because it is less letters. debbie

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 16 Apr, 2025 19:28
debbie	We won't merge the products. But I think it is reasonable to say they are the parts of whole. Bench data to support this would be great! I don't always call this, but in this case, I think it is a reasonable call. debbie

Link to this post | posted 16 Apr, 2025 19:17
debbie	Hi Nic, I think, but have little experimental evidence to support is that there is a frameshift between 42 and 43. So calling them both DNA methyltransferases is not a bad idea.Likely it is not functional without both parts. If 42 was not present, then I would not call a function for 43. Something to consider, debbie

Link to this post | posted 13 Apr, 2025 14:59
debbie	Excellent! Yes, plaques can definitely look different! debbie

Link to this post | posted 12 Apr, 2025 20:24

debbie

Hi Anne, Did you plate the control phage, Liebe, originally sent to you? If that infects and looks as expected, you should be fine. I believe we re-sent bacteria and the thought was that the bacteria you had was contaminated. Different phages can make different plaques, so that is OK. I am not sure what you are asking. So if you have more questions, let me know. With the bacteria we sent, you should re-hydrate and grow up a streak plate. Your cultures should always be made from a single colony. Do not continually repropagate from a liquid culture. I would also recommend as you grow up a culture to streak it out to make sure there is only one colony morphology and that it looks like what is expected. anything else? debbie