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

Link to this post | posted 08 Apr, 2025 11:04
debbie	Fred, I would call this Hypothetical Protein. The primary data sources have no hits. Also read the Glycosylation paper that describes the genes in Che8. https://pubmed.ncbi.nlm.nih.gov/37329881/ How many amino acids/domains are needs to be a glycosyltransferase? Best, debbie

Link to this post | posted 07 Apr, 2025 18:23
debbie	Thanks so much! Gold star for getting it re-blasted! best, debbie

Link to this post | posted 07 Apr, 2025 16:57
debbie	Randy, Is this so you can submit your genomes for QC? If you can't reBLAST on DNA Master, just record that on your annotation sheet and submit. best, debbie

Link to this post | posted 07 Apr, 2025 12:43

debbie

Hi! What are ribosomal proteins doing in phage genomes? https://www.nature.com/articles/s43705-022-00111-w And what accompanying factors could the phages encode? so many questions! Once you find a significant hit, refer to the Approved Function List to see if we have seen it before. Compare your hits to those to glean more information (if possible). If you find a differrent ribosomal protein, request a review by SMART and we can help to figure out what to add to the list. We will follow this paper for naming, https://pubmed.ncbi.nlm.nih.gov/24524803/ At present, we have 2 hit: bL12 and uL24. Good luck! debbie

Link to this post | posted 04 Apr, 2025 17:25
debbie	Hi all, updating will no longer work, but it has to be updated. Follow the directions on this forum post: https://seaphages.org/forums/topic/5577/