Link to this post | posted 27 Mar, 2025 17:16

debbie

Fred, Cluster F1 phages are notorious for the 1-4 base overlaps. The reason I like calling the shorter version of the glycosyltransferase is that it is supported by Starterator AND the HHPred doesn't show alignments in the upstream region of PDB glycosyltransferases. Check out the glycosylation paper about Che8. It should provide more information of best call. https://pubmed.ncbi.nlm.nih.gov/37329881/ debbie Remember that no one piece of data tells the story. It is when we put all of the pieces together that we can see best choices.

Link to this post | posted 26 Mar, 2025 11:34
debbie	Hi all, The GenBank file will need to include Hypothetical Protein or hypothetical protein. NKF will not be accepted. debbie

Link to this post | posted 24 Mar, 2025 15:21
debbie	Hi Ann, Yes, we can resend and depending on the dates of the MTA, no further paperwork is required. Would you send me an email for this (djs@pitt.edu). Please include your shipping address (and phone number), or confirm that information is on seaphages.org. Best, debbie

Link to this post | posted 13 Mar, 2025 12:15
debbie	Have you looked here? https://blast.ncbi.nlm.nih.gov/doc/blast-help/ There is a glossary of terms included there. Best, debbie

Link to this post | posted 12 Mar, 2025 16:01
debbie	Hi Kieran, I agree with your assessment. debbie

Link to this post | posted 11 Mar, 2025 20:27

debbie

Hi Fred, First, I believe the title of this inquiry is misplaced. There has never been a 5-rule cutoff. The text uses the word "typically" in the description, so, if you don't mind, I am going to change the title of this post. Next, your genome investigations are hitting the excellent work of Krista Freeman from the Hatfull Lab (soon to have her own lab at Case Western), where she has identified the various tail parts found in Mycobacterium phage Bxb1. Final revisions were accepted yesterday so we will have a paper(in Cell) to reference soon. The PDB for the structural proteins of Bxb1, but needs some tidying up. In the meantime, Here a bit of information to help guide: The tail tip project is PDB 9D93. (There are more projects for the tail tube and the capsid of Bxb1. TBD) 9D93_L: (A, B, C, D, E) is related to tail tube. This particular hit is hitting a small portion of a decoration domain of the tail tube, but NOT the important part of that decoration of the tail tube. Therefore, please call this one a Hypothetical Protein. However, the next gene, gp 24, stop at 25086, IS a hit to Bxb1's tail genes it hits Bxb1_gp34, the "tail wing brush". This is part of the PDB project 9D93_Q. Please use that terminology when calling this protein. And if you hit PDB project 9D93_J, you are hitting part of the tail tube (which we have historically called the major tail protein). More to come. The alpha-fold-chimera X views of all of this is extremely informative. Edited 11 Mar, 2025 20:31

Link to this post | posted 10 Mar, 2025 18:31

debbie

Hi Christy, Yep. It looks like the DNA Master website is down. (I've made an inquiry.) You can find the program that is needed in this forum post. the program is on Kristen Butela's One Drive. Kristen was posting a work around that is not needed, so get the program from her one drive and then closely follow the installation instructions found oh phagesDB. https://phagesdb.org/DNAMaster/ Best, debbie

Link to this post | posted 03 Mar, 2025 19:57

debbie

Shallee, in a perfect world. you can take 1ul of the sample, make some dilutions, and plate for single plaques. If that doesn't work, there are some additional considerations. (and of course you can start with more than 1ul.) Second step is to pick a single plaque and make a new working lysate, being sure to verify (maybe by pcr) that you have the phage you are interested in. debbie Edited 03 Mar, 2025 19:59

Link to this post | posted 26 Feb, 2025 20:50

debbie

Hi Lisa, In the regions where there are forward and reverse genes called, the previous annotators decided the evidence for forward genes i that region were more compelling. Please be sure to make you decisions based on the evidence that you have. Note that gene prediction models are using a 4 nucleotide sequence to find the most abundant patterns in the big open reading frames, then applying that pattern to the whole genome. The math will break down for smaller genes. My guess is that those regions where genes are called simultaneously on both strands are not very GC rich, so the patterns of ATCG are somewhat equivalent, so they are all getting called. Note to see if one of the programs (Glimmer or GeneMark) calls one strand more than the other. So you may see a bias due to the program's algorithm. debbie Edited 26 Feb, 2025 20:53

Link to this post | posted 26 Feb, 2025 20:46
debbie	It is not common but is definitely seen that Glimmer and GeneMark finds a big open reading frame on opposite strands and then calls most genes in that orientation. These genomes cannot have that many genes in their genomes. Caution is required as to where the other supporting data aligns. Look for the ORFs that have known phage function to build your case for where to call genes.